Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934
https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for
the disclosure.
Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572
https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_14.10' into release_15.01
Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844
https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.01' into release_15.03
Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2
https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.03' into release_15.05
Commit: 790e60af60093dcb8e26f093c3a87903605da206
https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.05' into release_15.07
Commit: 95daf69b372fa829325be561dc0a9907da0bea81
https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.07' into release_15.10
Commit: 4c07734f57453581666fd3994c44d583f3e319b9
https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.10' into release_16.01
Compare: https://github.com/galaxyproject/galaxy/compare/a274e635a6f7...4c07734f5745
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934
https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for
the disclosure.
Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572
https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_14.10' into release_15.01
Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844
https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.01' into release_15.03
Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2
https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.03' into release_15.05
Commit: 790e60af60093dcb8e26f093c3a87903605da206
https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.05' into release_15.07
Commit: 95daf69b372fa829325be561dc0a9907da0bea81
https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.07' into release_15.10
Commit: 4c07734f57453581666fd3994c44d583f3e319b9
https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.10' into release_16.01
Commit: 4cf70aea79772780b49dcdff08d63f40ca75ac6d
https://github.com/galaxyproject/galaxy/commit/4cf70aea79772780b49dcdff08d6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Compare: https://github.com/galaxyproject/galaxy/compare/788dc1ebef51...4cf70aea7977
Branch: refs/heads/release_16.07
Home: https://github.com/galaxyproject/galaxy
Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934
https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for
the disclosure.
Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572
https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_14.10' into release_15.01
Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844
https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.01' into release_15.03
Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2
https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.03' into release_15.05
Commit: 790e60af60093dcb8e26f093c3a87903605da206
https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.05' into release_15.07
Commit: 95daf69b372fa829325be561dc0a9907da0bea81
https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.07' into release_15.10
Commit: 4c07734f57453581666fd3994c44d583f3e319b9
https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.10' into release_16.01
Commit: 4cf70aea79772780b49dcdff08d63f40ca75ac6d
https://github.com/galaxyproject/galaxy/commit/4cf70aea79772780b49dcdff08d6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Commit: 22fda449f9d4ff2ed21fe4e39080456120aaf95e
https://github.com/galaxyproject/galaxy/commit/22fda449f9d4ff2ed21fe4e39080…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Compare: https://github.com/galaxyproject/galaxy/compare/602f2f2f1d43...22fda449f9d4
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: 75a3aecbbeddf7124ab9e6d7b885bdd28765e0e0
https://github.com/galaxyproject/galaxy/commit/75a3aecbbeddf7124ab9e6d7b885…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
Log Message:
-----------
Merge pull request #2820 from guerler/charts_revision
Charts revision, part 2
Commit: e8eb48a9c42de08edd6e9a4ea529bcac0d698df9
https://github.com/galaxyproject/galaxy/commit/e8eb48a9c42de08edd6e9a4ea529…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Remove unused app variable
Commit: f9758f2871e3b21b25d76f7b62bcc2aae99b9249
https://github.com/galaxyproject/galaxy/commit/f9758f2871e3b21b25d76f7b62bc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #2858 from martenson/rn_tweaks
alter release notes template
Commit: f98ade125f0fbe5d90ca0f005a84f8f7d91fb3d5
https://github.com/galaxyproject/galaxy/commit/f98ade125f0fbe5d90ca0f005a84…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
Log Message:
-----------
Add basic description for msa viewer
Commit: c4e9ecfe4c9dec4f9c58597fc755a4c4ab944a83
https://github.com/galaxyproject/galaxy/commit/c4e9ecfe4c9dec4f9c58597fc755…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/others/example/config.js
M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Allow multiple datatype matching
Commit: edfdef2853e2df3f5058d97e1578c4129fb292de
https://github.com/galaxyproject/galaxy/commit/edfdef2853e2df3f5058d97e1578…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Enhance ui menu button view
Commit: 633f958e1b6f2179264cdad06d9cda8cc13d0e93
https://github.com/galaxyproject/galaxy/commit/633f958e1b6f2179264cdad06d9c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Open tool executions in a different tab from admin/tool_lineage, instead of loading galaxy(whole) within the tab
Commit: 72f89a4c262de328d398ebbb4c6ccfefc483b75d
https://github.com/galaxyproject/galaxy/commit/72f89a4c262de328d398ebbb4c6c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Fix requirements message
Commit: ed76484af2ba5d86a9cfee82118f74dde70f21ae
https://github.com/galaxyproject/galaxy/commit/ed76484af2ba5d86a9cfee82118f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Fix toolbox's get_tool 'exact' matching. Previously it'd return a tool
even when exact was specified, though no exact match was made (so,
exact=False behavior, always)
Commit: c53585e8b5227e9d9f3536fa1434ae74acc0ef68
https://github.com/galaxyproject/galaxy/commit/c53585e8b5227e9d9f3536fa1434…
Author: zipho <zipho.m(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
added cProfile
Commit: d14b43abf2694ce3ef6933a9bede181ff1d7f79d
https://github.com/galaxyproject/galaxy/commit/d14b43abf2694ce3ef6933a9bede…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Probably still want to match identical tool guids against multiple sheds?
Commit: 66e3f8540f4dff918a90c2d02eca4a3f46f7fbdd
https://github.com/galaxyproject/galaxy/commit/66e3f8540f4dff918a90c2d02eca…
Author: zipho <zipho.m(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
removed traces of cProfile and use
Commit: d6639bee403a8cc79df647a21b79e905c3b6474d
https://github.com/galaxyproject/galaxy/commit/d6639bee403a8cc79df647a21b79…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
encourage wittiness in release notes
Commit: 4ad0bee5523b1a05423eaa21624ebe146412d423
https://github.com/galaxyproject/galaxy/commit/4ad0bee5523b1a05423eaa21624e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M doc/source/releases/16.07.rst
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Commit: c29f481dceeaaa790be1d8fdadfd58f1cb2d68c6
https://github.com/galaxyproject/galaxy/commit/c29f481dceeaaa790be1d8fdadfd…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/append_collection.xml
Log Message:
-----------
initial version of append collection tool. Allow's user to add one or more datasets to an existing collection. Provides options when we have name conflicts
Commit: b97ddd7ea52da1215c8251029f632cc972c6dba3
https://github.com/galaxyproject/galaxy/commit/b97ddd7ea52da1215c8251029f63…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M .ci/first_startup.sh
M .ci/flake8_lint_include_list.txt
M Makefile
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/library.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/reports.ini.sample
M config/tool_shed.ini.sample
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/dev/build_a_job_runner.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/queues.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/__init__.py
A lib/galaxy/util/postfork.py
M lib/galaxy/util/template.py
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/main.js
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M run.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/tool_shed/index.mako
A test/api/test_api_batch.py
M test/base/interactor.py
A test/casperjs/api-batch-tests.js
A test/functional/tools/dbkey_output_action.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_1.xml
A test/functional/tools/tool_provided_metadata_2.xml
A test/functional/tools/tool_provided_metadata_3.xml
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into collection_tools
Commit: 5159f878cfbdaa2627be76db1d69741b3579b68f
https://github.com/galaxyproject/galaxy/commit/5159f878cfbdaa2627be76db1d69…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M lib/galaxy/tools/append_collection.xml
Log Message:
-----------
change tool description
Commit: b1f4a0f61aeb8ddfec26c4b51bf92bdd50606c91
https://github.com/galaxyproject/galaxy/commit/b1f4a0f61aeb8ddfec26c4b51bf9…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Fix initial conda version at 4.0.5
This should prevent missing `activate` in <conda_prefix>/bin when
downgrading to 3.19.3. This is what the conda people use in their CI
environment (
[see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh…
and perhaps why that bug made it into the release in the first place).
Commit: f6c1aa0770508c552f074771078a4b7cc4cce400
https://github.com/galaxyproject/galaxy/commit/f6c1aa0770508c552f074771078a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Create a new trans method for getting the most recently touched history.
Swap several uses of get_history (with create=True, only), to use this
new functionality where it makes sense.
Commit: f88e8a19fa270615bdfe482ca4f2d1175f56d10b
https://github.com/galaxyproject/galaxy/commit/f88e8a19fa270615bdfe482ca4f2…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/append_collection.xml
Log Message:
-----------
changed tool name and description
Commit: f54bf1bb3b0afc28d948a511001895abcaf8b15f
https://github.com/galaxyproject/galaxy/commit/f54bf1bb3b0afc28d948a5110018…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
Now allow filter_failed_collection to accept and filter out list:paired collection
Commit: 97ba98037992a577a9a1a6b844893f63a7339034
https://github.com/galaxyproject/galaxy/commit/97ba98037992a577a9a1a6b84489…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
now change to see if the element has dataset_instance before attempting to call it.
Commit: 4729565dfdc32482b177e3e2740f8abcbc23ab0f
https://github.com/galaxyproject/galaxy/commit/4729565dfdc32482b177e3e2740f…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
added AppendCollectionTool to list of tool_classes
Commit: 9ff882944ee1fd78b6244dad5893ac7390eb76fa
https://github.com/galaxyproject/galaxy/commit/9ff882944ee1fd78b6244dad5893…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/masthead_test/static/script.js
M config/plugins/webhooks/phdcomics/helper/__init__.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webhooks/__init__.py
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
- unify webhooks entry point
- simlify webhooks code (on load)
- improve code readability
- clean up
Commit: d2ec87548a22273a2e0d94bbe1b415fbf6352b36
https://github.com/galaxyproject/galaxy/commit/d2ec87548a22273a2e0d94bbe1b4…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/webhooks.js
M templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
- add new entry point (Workflow)
- temporarily hide masthead webhook (due to instability)
Commit: d86ee3706089e59868c16a3352ce61e0257dbb40
https://github.com/galaxyproject/galaxy/commit/d86ee3706089e59868c16a3352ce…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Add the <conda_prefix> in 12. and fix typo
I am adding the ``<conda_prefix>/envs`` to check for the package to have been properly installed (if people have brought their own Conda).
And fixing ``conda_prefix`` to stay consistent in the doc (``<conda_prefix>``).
Commit: 040dd33980668ecb74a44dfc9c4e39e1a1339cef
https://github.com/galaxyproject/galaxy/commit/040dd33980668ecb74a44dfc9c4e…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M doc/source/admin/chat.rst
Log Message:
-----------
Fix typo
Commit: dbde38c951cdbb539def102ca55ddf5a4da3ced2
https://github.com/galaxyproject/galaxy/commit/dbde38c951cdbb539def102ca55d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M doc/source/admin/chat.rst
Log Message:
-----------
Merge pull request #2872 from remimarenco/patch-9
Fix typo
Commit: 569ceb4405bef72c420c91c86f4c203f6d7ed29f
https://github.com/galaxyproject/galaxy/commit/569ceb4405bef72c420c91c86f4c…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message:
-----------
Try reloading tool via control_task
Commit: 1223c420cb48ef05db61303ef784ff276716cdc3
https://github.com/galaxyproject/galaxy/commit/1223c420cb48ef05db61303ef784…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Explicitly monitor shed_tool_conf for changes
Commit: 1d04755fa39657bb824ca986e41224e77d59d35f
https://github.com/galaxyproject/galaxy/commit/1d04755fa39657bb824ca986e412…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Reference app instead of self when reloading toolbox
Commit: 6e4897dee7d66587d75b445f9211b51f07490241
https://github.com/galaxyproject/galaxy/commit/6e4897dee7d66587d75b445f9211…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Do not load individual new toolpanel elements (We rely on the tool watcher to reload the toolbox)
Commit: f7693802ce0d2e555cb283a09d0a83740e8664e2
https://github.com/galaxyproject/galaxy/commit/f7693802ce0d2e555cb283a09d0a…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Remove in-memory removal of tools (rely on toolbox reload)
Commit: 7b259fb10a5f1289ba81ec749a1e86ccf3fb7303
https://github.com/galaxyproject/galaxy/commit/7b259fb10a5f1289ba81ec749a1e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Remove one more unused panel manipulation function
Commit: 128ee9b72a6c7f693a990c65b1c4b34d9be193c5
https://github.com/galaxyproject/galaxy/commit/128ee9b72a6c7f693a990c65b1c4…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Remove unused variable
Commit: 81bf7b382bc1003c0d1a3b0a019ea7e57d6ecce9
https://github.com/galaxyproject/galaxy/commit/81bf7b382bc1003c0d1a3b0a019e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M test/unit/tools/test_watcher.py
Log Message:
-----------
Start conf_watcher thread in unit tests
Commit: e340fd4e06f7b8a2063448bad8e2c594af39cdb9
https://github.com/galaxyproject/galaxy/commit/e340fd4e06f7b8a2063448bad8e2…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M test/unit/tools/test_watcher.py
Log Message:
-----------
Wait before triggering a callback in test_watcher.py
Commit: 3206421b91a305d1e38672a1bccd52c732705266
https://github.com/galaxyproject/galaxy/commit/3206421b91a305d1e38672a1bccd…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Remove update_shed_conf test
We do not update the toolbox in memory, so this test is obsolete
Commit: fe158de11109140b22c408cd6640b547ffd4db30
https://github.com/galaxyproject/galaxy/commit/fe158de11109140b22c408cd6640…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Remove panel_manager tests for deactivated tools
Deactivate tests that rely on deactivating, but not removing entries
from tool_conf. For tests that test changes in tool_panel, load a new
toolbox after making the changes.
Commit: ad86e2c7840fa9129263fdfb144959c158653874
https://github.com/galaxyproject/galaxy/commit/ad86e2c7840fa9129263fdfb1449…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
Log Message:
-----------
Add sleep to allow toolbox to finish loading
Commit: ded1db8b3834bf3de6897b2163a9d208828d259d
https://github.com/galaxyproject/galaxy/commit/ded1db8b3834bf3de6897b2163a9…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
Log Message:
-----------
Remove test for deactivated tools and sections
These are tests that verify that deactivated tools were present in the
correct tool panel section.
Commit: 579ea41085501139eebbbeb5b3f72c9c04c03e4c
https://github.com/galaxyproject/galaxy/commit/579ea41085501139eebbbeb5b3f7…
Author: Rémi Marenco <remi.marenco(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Update Marius advice
Commit: e6450369730230bc844db67d3df05f1cffd3cdad
https://github.com/galaxyproject/galaxy/commit/e6450369730230bc844db67d3df0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Merge pull request #2871 from remimarenco/patch-8
Add the <conda_prefix> in 12. and fix typo
Commit: 0bd1ea108e7f6000759583afd3e6d2d7daa3e7be
https://github.com/galaxyproject/galaxy/commit/0bd1ea108e7f6000759583afd3e6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Merge pull request #2870 from dannon/histories.most_recent_v_default
Create a new trans method for getting the most recently touched history.
Commit: ba6a0a36476cd5db46777e99b84b6440ec6073b0
https://github.com/galaxyproject/galaxy/commit/ba6a0a36476cd5db46777e99b84b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Merge pull request #2869 from mvdbeek/upgrade_conda_instead_of_downgrading
Fix initial conda version at 4.0.5
Commit: 19a09e18a84a860d60e66517b3b68b58628843c7
https://github.com/galaxyproject/galaxy/commit/19a09e18a84a860d60e66517b3b6…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
R lib/galaxy/tools/append_collection.xml
Log Message:
-----------
removed append_collection tool due to John request. MergeCollection should cover all cases that append would have anyway.
Commit: 59852d0e0f4897b09a964091d5792458de48deb0
https://github.com/galaxyproject/galaxy/commit/59852d0e0f4897b09a964091d579…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
R config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png
R config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/components/jobs.js
R config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js
R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js
R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js
R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
M config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Use remote repo for chart plugins
Commit: 54e589ebad000535c384850df7abe6c195fbe5f5
https://github.com/galaxyproject/galaxy/commit/54e589ebad000535c384850df7ab…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
Log Message:
-----------
Merge pull request #2769 from davebx/api_install_performance
Cleanup of and performance enhancements to the API installation of repositories.
Commit: af45adb7e6e57d4180b49581c5f48274df54117f
https://github.com/galaxyproject/galaxy/commit/af45adb7e6e57d4180b49581c5f4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add error message if charts fails to retrieve plugin resources from its repository
Commit: 3e7302fc3c6d8f0713d8698f6536662fc46f42b0
https://github.com/galaxyproject/galaxy/commit/3e7302fc3c6d8f0713d8698f6536…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Fix remote url
Commit: 5ebdefe40f1d816339c21f553cbe67365a9d7285
https://github.com/galaxyproject/galaxy/commit/5ebdefe40f1d816339c21f553cbe…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
Log Message:
-----------
Merge pull request #2862 from dannon/fix_lineage_onclick
Open tool executions in a different tab from admin/tool_lineage, inst…
Commit: ecc415369ff50dce02f5db73bdaf6fe8e60b6020
https://github.com/galaxyproject/galaxy/commit/ecc415369ff50dce02f5db73bdaf…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
Log Message:
-----------
added support to merge two list:paired collection together. Added single test to reflect new changes.
Commit: 693eb5d0c91061fdbe052b41be1e78f4c58f57cb
https://github.com/galaxyproject/galaxy/commit/693eb5d0c91061fdbe052b41be1e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
Log Message:
-----------
Wait 2 seconds after touch shed_tool_conf.xml
The file watcher monitors for changes every second, so 2 seconds should
be enough to let tests that check the tool panel after installing new
tools pass.
Commit: 2fb4045abd61b9ccb1afb4e5e422ad6e73167db8
https://github.com/galaxyproject/galaxy/commit/2fb4045abd61b9ccb1afb4e5e422…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/data_manager/manager.py
Log Message:
-----------
Also reload data managers upon touching data_manager.conf
Commit: f6fc5ed44299f2d1a9ac1c966d43281fd9515bf0
https://github.com/galaxyproject/galaxy/commit/f6fc5ed44299f2d1a9ac1c966d43…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/data_manager/manager.py
Log Message:
-----------
Shut down old data manager watchers
Commit: abd4fa611a3f1d4d089a03aef48ecb43383bb101
https://github.com/galaxyproject/galaxy/commit/abd4fa611a3f1d4d089a03aef48e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Implement hashing for tool conf watcher
If modification time of watched files changes, only trigger event if
hashes differ as well
Commit: 49ab74827cd0905cd0fa62eee7a5643b43ad41d9
https://github.com/galaxyproject/galaxy/commit/49ab74827cd0905cd0fa62eee7a5…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Log who's triggering a reload
Commit: a2669c565ae7c25bcd20c9831a470bbc0731597c
https://github.com/galaxyproject/galaxy/commit/a2669c565ae7c25bcd20c9831a47…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Add back integrated_tool_panel saving
Commit: 6fc46a8c46549bc43fca00cfbd2e32b07db158d5
https://github.com/galaxyproject/galaxy/commit/6fc46a8c46549bc43fca00cfbd2e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Directly reload toolbox or data manager when watcher triggers reload
Commit: 054fbd05cb2ca3918f0dd2819cc71e5485ef4580
https://github.com/galaxyproject/galaxy/commit/054fbd05cb2ca3918f0dd2819cc7…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Use the tool_data_tables.tool_data_path, to avoid persisting the temporary in-memory path to the data table
Commit: 612eea85e6e2322d277f4210005d2efbddaae3e1
https://github.com/galaxyproject/galaxy/commit/612eea85e6e2322d277f4210005d…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Fix reload thread for uwsgi workers.
and fix typos
Commit: 1bc84e0b4f5a77d018126656fc2808ed66c4712e
https://github.com/galaxyproject/galaxy/commit/1bc84e0b4f5a77d018126656fc28…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Do not call start() method of watchter
as this happens when it starts watching a file.
Commit: b8695b36280f195242215c56cffad9aff5a7fad4
https://github.com/galaxyproject/galaxy/commit/b8695b36280f195242215c56cffa…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
One last attempt to revive launched thread
Commit: 9e36a15e22f92fd3913a1dbed0700bcae91b61e7
https://github.com/galaxyproject/galaxy/commit/9e36a15e22f92fd3913a1dbed070…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Transplant tool conf watcher thread
Commit: 95c0e3cbf78e45f7786cab918835004dc67c156d
https://github.com/galaxyproject/galaxy/commit/95c0e3cbf78e45f7786cab918835…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/data_manager/manager.py
Log Message:
-----------
Also reload conf_watchers for data managers
Commit: c0cef19eb7a68e61ac30d9eb55b6bef14705648d
https://github.com/galaxyproject/galaxy/commit/c0cef19eb7a68e61ac30d9eb55b6…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Reload data managers after reloading the toolbox
Commit: 3d42be5f234d837ff5fa3792c53d138d3e28fcac
https://github.com/galaxyproject/galaxy/commit/3d42be5f234d837ff5fa3792c53d…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/watcher.py
Log Message:
-----------
Trigger event with lock
Commit: 42854e31ea50eae1e26ce2112696cd86ccb247be
https://github.com/galaxyproject/galaxy/commit/42854e31ea50eae1e26ce2112696…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Bundle thumbnail view
Commit: d4d403d678a9c6d5a5dbf1df5c23b8425f1a1311
https://github.com/galaxyproject/galaxy/commit/d4d403d678a9c6d5a5dbf1df5c23…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Show list instead
Commit: 6f444e5cdbc69ba0fdca4a04c1dce7d7493420be
https://github.com/galaxyproject/galaxy/commit/6f444e5cdbc69ba0fdca4a04c1dc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Restore regular selection view
Commit: ccd265ed0705d3166f792d7d1473f229c8b5accb
https://github.com/galaxyproject/galaxy/commit/ccd265ed0705d3166f792d7d1473…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix tab creation behavior
Commit: d65bf1e4f773c6c6d27b83e7a850b51bfd3d3faa
https://github.com/galaxyproject/galaxy/commit/d65bf1e4f773c6c6d27b83e7a850…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix sorting
Commit: bee75fb77909ddc938290c134eb689a7f5729254
https://github.com/galaxyproject/galaxy/commit/bee75fb77909ddc938290c134eb6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix order
Commit: 9601a0f607b71e8725dafff90288ee8486dbfcf1
https://github.com/galaxyproject/galaxy/commit/9601a0f607b71e8725dafff90288…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Revise thumbnail view
Commit: ec038cb0904b24c6df8cb5f7b16e671997004aa7
https://github.com/galaxyproject/galaxy/commit/ec038cb0904b24c6df8cb5f7b16e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Use original order
Commit: 5cae6f7735436800c586065be690a43c1a1683e5
https://github.com/galaxyproject/galaxy/commit/5cae6f7735436800c586065be690…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix spacing
Commit: 71fe20ab040df9393c8ac0c083a31006a65ab848
https://github.com/galaxyproject/galaxy/commit/71fe20ab040df9393c8ac0c083a3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M client/galaxy/scripts/utils/utils.js
M config/plugins/visualizations/charts/static/views/description.js
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/utils/utils.js
Log Message:
-----------
Identify links in visualizations plugins descriptions
Commit: e0617bb29b280f5f7f756ccbfdd6678ed3e185ef
https://github.com/galaxyproject/galaxy/commit/e0617bb29b280f5f7f756ccbfdd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Add tooltip to thumbnail view?
Commit: f03a06488feb0e1c471c92d11cff14c6bf5c0cf1
https://github.com/galaxyproject/galaxy/commit/f03a06488feb0e1c471c92d11cff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Limit title length for thumbnails
Commit: f2b26a61cb14ff468ecc2971d6394e6cea64f889
https://github.com/galaxyproject/galaxy/commit/f2b26a61cb14ff468ecc2971d639…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Filter suitable visualization types on initialization
Commit: 84942582b57499a753cf9e8039486c3bc9efa4f3
https://github.com/galaxyproject/galaxy/commit/84942582b57499a753cf9e803948…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
Log Message:
-----------
Modify error message
Commit: 3e79da902163b131aff677a7b1bad9fa87e61d89
https://github.com/galaxyproject/galaxy/commit/3e79da902163b131aff677a7b1ba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Fix error messages
Commit: bc1be68bb6f0eef840465dd2b578136d0094ae20
https://github.com/galaxyproject/galaxy/commit/bc1be68bb6f0eef840465dd2b578…
Author: zipho <zipho.m(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
added the extra blank line
Commit: e85cd284d099af16329d6592b46dc3d6ce37dba4
https://github.com/galaxyproject/galaxy/commit/e85cd284d099af16329d6592b46d…
Author: zipho <zipho.m(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/library_common.py
Log Message:
-----------
fixed the line tabs
Commit: 271959d1345077baa064c60fe79ff00a6ed0b021
https://github.com/galaxyproject/galaxy/commit/271959d1345077baa064c60fe79f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/tool_shed/metadata/metadata_generator.py
M test/unit/tools/test_watcher.py
Log Message:
-----------
Reload data table managers and data tables
... before reloading data managers. Data managers need to have access to
the data tables, so that they can process the results.
Do not explicitly start watcher thread for shed_data_manager_conf
changes.
Commit: f92d496bd9ae42387e5017e2ef84a032de6e49ea
https://github.com/galaxyproject/galaxy/commit/f92d496bd9ae42387e5017e2ef84…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Remove debugging statements and mention uwsgi/threads in line
Commit: 7afb25d5fbf8bcb37d4c9fc7e25b20b8d8373011
https://github.com/galaxyproject/galaxy/commit/7afb25d5fbf8bcb37d4c9fc7e25b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Wait for shed_data_manager_conf watcher to pick up changes
Commit: 1a2e34561aa634de4ff1a4d793e32de1d1ff316e
https://github.com/galaxyproject/galaxy/commit/1a2e34561aa634de4ff1a4d793e3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
R lib/galaxy/tools/toolbox/requirements.py
Log Message:
-----------
Remove empty file in toolbox module.
Assuming it was accidentally added by @mvdbeek in 753587931ed3a460e57334de398d5048bc35f6b9.
Commit: 75d2c0eac7a320a06ac1173045606fbd4bfbff72
https://github.com/galaxyproject/galaxy/commit/75d2c0eac7a320a06ac117304560…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/util/filelock.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
Log Message:
-----------
Refactor - move filelock.py to galaxy.util.
galaxy.tools.deps.resolvers.conda should not depend on galaxy.web.proxy - this is a smell that indicates filelock belongs in galaxy.util IMO.
Commit: 7b44cc5470728b59a2b47c64aedd27774706dd8b
https://github.com/galaxyproject/galaxy/commit/7b44cc5470728b59a2b47c64aedd…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M Makefile
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M scripts/bootstrap_history.py
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/index.mako
A test/api/test_api_batch.py
A test/casperjs/api-batch-tests.js
Log Message:
-----------
Merge branch 'dev' into bbi-js3
Commit: c09bd5688a8adb309df33049fd3c8cee0e6b80ac
https://github.com/galaxyproject/galaxy/commit/c09bd5688a8adb309df33049fd3c…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M Makefile
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/reports.ini.sample
M config/tool_shed.ini.sample
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/postfork.py
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/tool_shed/config.py
M scripts/bootstrap_history.py
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/index.mako
A test/api/test_api_batch.py
A test/casperjs/api-batch-tests.js
Log Message:
-----------
Merge remote branch 'upstream/dev' into dev
Commit: 5d780d68d1a2ec5d1928a0156637a1d522f5b743
https://github.com/galaxyproject/galaxy/commit/5d780d68d1a2ec5d1928a0156637…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/screenshot.js
Log Message:
-----------
Revise exporting functions, increase png quality, remove unused libraries
Commit: 0d160900ace430f370330a3343e3c3ed79c78450
https://github.com/galaxyproject/galaxy/commit/0d160900ace430f370330a3343e3…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
R database/info.txt
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
Log Message:
-----------
Merge pull request #2808 from sszakony/dev
Addressing issue 2747, login appearing in scratchbook window
Commit: 78bd9e8f867eb5747218644e2a5a1f5417079b73
https://github.com/galaxyproject/galaxy/commit/78bd9e8f867eb5747218644e2a5a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M Makefile
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
R database/info.txt
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M scripts/bootstrap_history.py
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/index.mako
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 3908a9a8361da77427392b7d90a1ace780839cc2
https://github.com/galaxyproject/galaxy/commit/3908a9a8361da77427392b7d90a1…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
R lib/galaxy/tools/toolbox/requirements.py
Log Message:
-----------
Merge pull request #2877 from jmchilton/remove_empty_file
Remove empty file in toolbox module.
Commit: 5518c20a20e6fc38ac1edfbbdaa2a8a4f1737c95
https://github.com/galaxyproject/galaxy/commit/5518c20a20e6fc38ac1edfbbdaa2…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Cleanup: (a) remove debugging statements; (b) use Galaxy app; and (c) fix offset issue for LinePainter using floor instead of ceil.
Commit: a97b4bae546a5621dc37b6beaaba747d51c8ed9e
https://github.com/galaxyproject/galaxy/commit/a97b4bae546a5621dc37b6beaaba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
Log Message:
-----------
Rename types to registry to avoid confusion
Commit: 494141c260514071c5187a83a8dd1700643b5423
https://github.com/galaxyproject/galaxy/commit/494141c260514071c5187a83a8dd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Use underscores for internal parameters to avoid conflicts
Commit: 61839637f098130ccd54bfe408ff9955dbffc883
https://github.com/galaxyproject/galaxy/commit/61839637f098130ccd54bfe408ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/storage.js
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Simplify storage handling
Commit: 7d20e9055e1be434c7914fc540ceb64a8e4d1051
https://github.com/galaxyproject/galaxy/commit/7d20e9055e1be434c7914fc540ce…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
Log Message:
-----------
Remove unused options variable
Commit: a19f67f8be85c4d5b459082ea9343cbda0a298b3
https://github.com/galaxyproject/galaxy/commit/a19f67f8be85c4d5b459082ea934…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Try locking load_item
Commit: 426ea3b726a085f1a89033ed875584468db7b321
https://github.com/galaxyproject/galaxy/commit/426ea3b726a085f1a89033ed8755…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Keep a count of reloads
Commit: c4aa171ae4bc16667b082122ef14dfc0f08891c8
https://github.com/galaxyproject/galaxy/commit/c4aa171ae4bc16667b082122ef14…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/data_manager/manager.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Always wait for reload action to be finished
Commit: 55cd6d86333b63747c257911a16a68a42bb34828
https://github.com/galaxyproject/galaxy/commit/55cd6d86333b63747c257911a16a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
A lib/galaxy/util/filelock.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
Log Message:
-----------
Merge pull request #2879 from jmchilton/refactor_filelock
Refactor - move filelock.py to galaxy.util.
Commit: 7f893f39f6d1087afe50af9d9a61da77fcbe14db
https://github.com/galaxyproject/galaxy/commit/7f893f39f6d1087afe50af9d9a61…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M test/unit/tools_support.py
Log Message:
-----------
Mock the Lock; fix linting problems
Commit: c1d66d1fbc7281cb2cd5b050e8516818093d3e6a
https://github.com/galaxyproject/galaxy/commit/c1d66d1fbc7281cb2cd5b050e851…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M test/unit/tools_support.py
Log Message:
-----------
One more linting fix
Commit: 4adc872e5864d9a8262948a56a4552fbafe68390
https://github.com/galaxyproject/galaxy/commit/4adc872e5864d9a8262948a56a45…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M test/unit/tools_support.py
Log Message:
-----------
Fix indentation
Commit: 30d4e338b473797816e8b8a5da93dcd5420e24fc
https://github.com/galaxyproject/galaxy/commit/30d4e338b473797816e8b8a5da93…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Revise visualization config handling
Commit: 57b41b201964b57daf9a95c06120cbe1bba14e1b
https://github.com/galaxyproject/galaxy/commit/57b41b201964b57daf9a95c06120…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
Log Message:
-----------
Fix chart saving
Commit: 22e79f7aa943edb9ca6a80d1b035931ab8c9232f
https://github.com/galaxyproject/galaxy/commit/22e79f7aa943edb9ca6a80d1b035…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Improve handling for cases with missing plugins
Commit: 21ccf76b1009301365171d7a33afb380b40dd3a3
https://github.com/galaxyproject/galaxy/commit/21ccf76b1009301365171d7a33af…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
API, history contents: contents download endpoint
- Adds an api endpoint at 'histories/{id}/contents/archive' for
creating an archive from all history contents or a filtered subset
of contents
- Contents are returned in 'tgz' format currently
- Datasets are located in the archive in paths roughly matching the
nesting relationships of their parent collections
- Filters can be applied using the same syntax as index
- Adding 'dry_run=True' will return a JSON list of archive paths and
dataset file paths for debugging
- Adds map_datasets method for walking the datasets of histories and
HDCAs
Commit: 76c9948742d659b2dd73452cc2d3c49f44f00cd7
https://github.com/galaxyproject/galaxy/commit/76c9948742d659b2dd73452cc2d3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Enhance notification and handling when chart type is unavailable
Commit: 81dffca58cab841dfcf0fda42b42d5c97f54f245
https://github.com/galaxyproject/galaxy/commit/81dffca58cab841dfcf0fda42b42…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Remove test case, replace change listeners
Commit: fa7930d20e10309aee666f280963b759571e3884
https://github.com/galaxyproject/galaxy/commit/fa7930d20e10309aee666f280963…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix message persistence for missing column notification
Commit: b3451ed03d5104442b4935905e330b006e492204
https://github.com/galaxyproject/galaxy/commit/b3451ed03d5104442b4935905e33…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix message persistence for missing data groups
Commit: 4669d5ee26410faec0c6e49aed512352631066e3
https://github.com/galaxyproject/galaxy/commit/4669d5ee26410faec0c6e49aed51…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Remove warning notification when leaving charts, data is saved upon drawing
Commit: 00053b6d30b21ce2eed5419a3537caa0b8cd7797
https://github.com/galaxyproject/galaxy/commit/00053b6d30b21ce2eed5419a3537…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
Log Message:
-----------
Fix spacing
Commit: ffba835195737c4705e5b2717c384be05edeae91
https://github.com/galaxyproject/galaxy/commit/ffba835195737c4705e5b2717c38…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Remove spacing
Commit: 99acb36da32ec2d2d4d7d1ce7cdc4da426e51645
https://github.com/galaxyproject/galaxy/commit/99acb36da32ec2d2d4d7d1ce7cdc…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M test/unit/tools_support.py
Log Message:
-----------
Add server_name to unit test app's config.
Required for messaging stuff.
Commit: 7351d67967a0750a5e351660b457d92dcb01b516
https://github.com/galaxyproject/galaxy/commit/7351d67967a0750a5e351660b457…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Remove unused listener
Commit: 9f7c749638340fb63ac00a417a9e328875296885
https://github.com/galaxyproject/galaxy/commit/9f7c749638340fb63ac00a417a9e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/tools/toolbox/base.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M test/unit/tools_support.py
Log Message:
-----------
Fix test case for tool manager.
Commit: 05fa9b9f5adcd96456348754225c72554d4e12af
https://github.com/galaxyproject/galaxy/commit/05fa9b9f5adcd96456348754225c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Rename remote to repository to avoid confusion
Commit: 3d9df6437073484d243d64fc9606dc137dc6bfb7
https://github.com/galaxyproject/galaxy/commit/3d9df6437073484d243d64fc9606…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Rename optional config attributes name accordingly
Commit: efac63f7cd5a46a26eb9f27a78510f06e072b6b9
https://github.com/galaxyproject/galaxy/commit/efac63f7cd5a46a26eb9f27a7851…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
A database/info.txt
Log Message:
-----------
Restore database/info.txt.
It was problematically removed with a recent PR and is causing Travis breakages - Galaxy assumes this directory exists.
Commit: 50c8302b1525ebc2168bb0a9ab4439105d9317e7
https://github.com/galaxyproject/galaxy/commit/50c8302b1525ebc2168bb0a9ab44…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/tools/cwl/parser.py
Log Message:
-----------
Small cwl fixes to sync with galaxy-lib.
description became doc in draft 1.0.
Commit: 0d35f9435ad6d9cd1636d7626dae97ad8d08027d
https://github.com/galaxyproject/galaxy/commit/0d35f9435ad6d9cd1636d7626dae…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
A database/info.txt
Log Message:
-----------
Merge pull request #2887 from jmchilton/database_info_restore
Restore database/info.txt.
Commit: 07cf96c26053d8a0d0fe1a6365f6bf4272a3593d
https://github.com/galaxyproject/galaxy/commit/07cf96c26053d8a0d0fe1a6365f6…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Update Conda FAQ
Commit: 9a9a1f9becf185db5a778f1436913bc6942b2ac3
https://github.com/galaxyproject/galaxy/commit/9a9a1f9becf185db5a778f143691…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Lint for last commit.
Commit: 4479bcebbe6984c06d0b5b9411d6d9e8bc2f22ca
https://github.com/galaxyproject/galaxy/commit/4479bcebbe6984c06d0b5b9411d6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M doc/source/admin/conda_faq.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
R lib/galaxy/tools/toolbox/requirements.py
A lib/galaxy/util/filelock.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into reload_toolbox_across_handlers
Commit: b1940945607448f3795f98f6ffd8c8dd37c7b3d5
https://github.com/galaxyproject/galaxy/commit/b1940945607448f3795f98f6ffd8…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
Changed wording on common.mako when selecting how to install tool and handle dependencies
Commit: a199590efa2378e2f1f865b8da68cc4fe12a33c1
https://github.com/galaxyproject/galaxy/commit/a199590efa2378e2f1f865b8da68…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/tools/cwl/parser.py
Log Message:
-----------
Merge pull request #2888 from jmchilton/cwl_fixes_from_lib
Small cwl fixes to sync with galaxy-lib.
Commit: ecdbf4d0b579f4dbae79a56aea1398224d9f2c93
https://github.com/galaxyproject/galaxy/commit/ecdbf4d0b579f4dbae79a56aea13…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Address PR #2891 comments
Commit: 53d387d771b3bb95cd17cf0c74ec90099122f376
https://github.com/galaxyproject/galaxy/commit/53d387d771b3bb95cd17cf0c74ec…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Another linting fix.
Commit: ff301c562b87a1843d18819eb79dd580d207e9c8
https://github.com/galaxyproject/galaxy/commit/ff301c562b87a1843d18819eb79d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add debug log, fix config name, add comment for local repository
Commit: 36c1384d020bcb2d3a89da83861cccfae23e8916
https://github.com/galaxyproject/galaxy/commit/36c1384d020bcb2d3a89da83861c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Use rawgit for proper MIME type handling
Commit: 819cb65d2e1ecc905b22e97b9972fa8901ac09c1
https://github.com/galaxyproject/galaxy/commit/819cb65d2e1ecc905b22e97b9972…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add repository revision to url
Commit: 3cee333011bff6aed673429f361659132804f33c
https://github.com/galaxyproject/galaxy/commit/3cee333011bff6aed673429f3616…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M lib/galaxy/tools/cwl/parser.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into dev
Commit: 97b748c73a4eb169c5e1c6894ea2b30dbcc0343a
https://github.com/galaxyproject/galaxy/commit/97b748c73a4eb169c5e1c6894ea2…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Shorten Conda environment naming as per https://github.com/galaxyproject/galaxy/commit/e9d81500caa3526200b204270aca…
Thanks @lparsons.
Commit: d5440f7ac4170adf27f757fdfbc888a67e20cf27
https://github.com/galaxyproject/galaxy/commit/d5440f7ac4170adf27f757fdfbc8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository version, allow pdb rendering type selection
Commit: 14ef3e3d448dc4190707312443b6f60e187ee962
https://github.com/galaxyproject/galaxy/commit/14ef3e3d448dc4190707312443b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository version
Commit: 2b6b5c82754a3ca9722e55d9828042e70d95d028
https://github.com/galaxyproject/galaxy/commit/2b6b5c82754a3ca9722e55d98280…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
Log Message:
-----------
Merge pull request #2891 from afgane/dev
Update Conda FAQ
Commit: cd8daaab1f30fd0a45dd4903d0d3de2c9ed5633b
https://github.com/galaxyproject/galaxy/commit/cd8daaab1f30fd0a45dd4903d0d3…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
Merge pull request #2893 from nturaga/change_dependency_wording
Changed wording on common.mako when selecting how to install tool and…
Commit: 5483e9f5bf4d725e3bb2a746db1d9c1a911a5291
https://github.com/galaxyproject/galaxy/commit/5483e9f5bf4d725e3bb2a746db1d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Fix indention for noscratchbook flag
Commit: fed59596a37176b388d74346cd7fce6bba224c8e
https://github.com/galaxyproject/galaxy/commit/fed59596a37176b388d74346cd7f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Fix the infinite loop.
Thanks @mvdbeek!
Commit: afefb9dd831ff5aed21c74cc159dc6d62eebe64a
https://github.com/galaxyproject/galaxy/commit/afefb9dd831ff5aed21c74cc159d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge pull request #2894 from guerler/revise_noscratchbook_flag
Fix indention for noscratchbook flag
Commit: d98a72d58e1cf462eb89f4a9cd3e04a5c6fea9fb
https://github.com/galaxyproject/galaxy/commit/d98a72d58e1cf462eb89f4a9cd3e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A database/info.txt
M doc/source/admin/conda_faq.rst
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/deps/resolvers/conda.py
R lib/galaxy/tools/toolbox/requirements.py
A lib/galaxy/util/filelock.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js.map
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 61fb26181c7dfaefa821f616171a281928153b70
https://github.com/galaxyproject/galaxy/commit/61fb26181c7dfaefa821f616171a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools_support.py
Log Message:
-----------
Merge pull request #2840 from mvdbeek/reload_toolbox_across_handlers
Allow reloading tools without restarting galaxy, simplify tool panel handling for tool shed installed tools
Commit: d092bd8ec2d29bd05a701c0edae1c915e392d257
https://github.com/galaxyproject/galaxy/commit/d092bd8ec2d29bd05a701c0edae1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Enable new run workflow form by default
Commit: e510f86a05b2a8ad368e0b99f521bfcce207cfc1
https://github.com/galaxyproject/galaxy/commit/e510f86a05b2a8ad368e0b99f521…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Update default value in sample config file
Commit: 0c8dadcede0609ed1a8aed997c57adceaf8dce83
https://github.com/galaxyproject/galaxy/commit/0c8dadcede0609ed1a8aed997c57…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-06 (Tue, 06 Sep 2016)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Seemingly fix #2806.
I guess this would make sense if somehow the step of this workflow has its tool parameters double wrapped.
Commit: cbd55b20d373538d2b8019344dd08a0fd190752c
https://github.com/galaxyproject/galaxy/commit/cbd55b20d373538d2b8019344dd0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-06 (Tue, 06 Sep 2016)
Changed paths:
M config/galaxy.ini.sample
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Merge pull request #2895 from guerler/activate_new_run_form
Enable new run workflow form
Commit: b710ed1e8519fc6ed85f1d9cef4b63e679294a93
https://github.com/galaxyproject/galaxy/commit/b710ed1e8519fc6ed85f1d9cef4b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-06 (Tue, 06 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix over encoding of dataset ids
Commit: 94338632e005da8a9e90eabdbf915b9102b9308e
https://github.com/galaxyproject/galaxy/commit/94338632e005da8a9e90eabdbf91…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-07 (Wed, 07 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Rename lda id parameter
Commit: d6b9348f377d48f85286fdf57b826ec99e29a856
https://github.com/galaxyproject/galaxy/commit/d6b9348f377d48f85286fdf57b82…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-07 (Wed, 07 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dockerfiles.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M setup.cfg
M test/unit/test_objectstore.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Extend import order linting to all of galaxy-lib w/fixes.
Includes a bit linting of order for galaxy.util.
Commit: 825c7287a57dabe465f86bb5b66730aba080d000
https://github.com/galaxyproject/galaxy/commit/825c7287a57dabe465f86bb5b667…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-07 (Wed, 07 Sep 2016)
Changed paths:
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/util/topsort.py
Log Message:
-----------
Lint fixes thanks to @nsoranzo's eagle eyes.
Commit: 259e6730c21dae72c6bd60ba38b52f6954b9ca83
https://github.com/galaxyproject/galaxy/commit/259e6730c21dae72c6bd60ba38b5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-07 (Wed, 07 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Rename to use_security
Commit: 69ee5afaeca5dce6acb814cf292a009e9fd2f0c5
https://github.com/galaxyproject/galaxy/commit/69ee5afaeca5dce6acb814cf292a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-07 (Wed, 07 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dockerfiles.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M setup.cfg
M test/unit/test_objectstore.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Merge pull request #2889 from jmchilton/import-order-linting
Extend import order linting to all of galaxy-lib w/fixes.
Commit: 2d36ab52dee7085628f30ecd58c7c920158804d8
https://github.com/galaxyproject/galaxy/commit/2d36ab52dee7085628f30ecd58c7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-07 (Wed, 07 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #2902 from guerler/fix_id_storage
Fix over encoding of dataset ids
Commit: d5ba73b0c84f6bfa297d4b75296e5614d25a07cf
https://github.com/galaxyproject/galaxy/commit/d5ba73b0c84f6bfa297d4b75296e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
Log Message:
-----------
Fix hang when installing data managers
Commit: 82c1da4709a5ae5b52ee60b2b197f91d64c5d5d3
https://github.com/galaxyproject/galaxy/commit/82c1da4709a5ae5b52ee60b2b197…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Add data managers to new toolbox
before replacing the old toolbox, to avoid 'Tool not found or not
accessible.' while installing new tools
Commit: a8f794290dc1e529dd9564a95a55f4b808b2e6d9
https://github.com/galaxyproject/galaxy/commit/a8f794290dc1e529dd9564a95a55…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Handle xml ParseError
Occasionally the following Traceback can be seen in the log files:
```
Traceback (most recent call last):
File "lib/galaxy/tools/toolbox/base.py", line 112, in
_init_tools_from_configs
self._init_tools_from_config( config_filename )
File "lib/galaxy/tools/toolbox/base.py", line 136, in
_init_tools_from_config
tool_conf_source = get_toolbox_parser(config_filename)
File "lib/galaxy/tools/toolbox/parser.py", line 152, in
get_toolbox_parser
return XmlToolConfSource(config_filename)
File "lib/galaxy/tools/toolbox/parser.py", line 40, in __init__
tree = parse_xml(config_filename)
File "lib/galaxy/util/__init__.py", line 210, in parse_xml
root = tree.parse( fname, parser=ElementTree.XMLParser(
target=DoctypeSafeCallbackTarget() ) )
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse
self._root = parser.close()
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in
close
self._raiseerror(v)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in
_raiseerror
raise err
ParseError: unclosed token: line 2636, column 0
```
We just try parsing again, which seems to solve the issue.
This may be a problem with concurrently reading/writing to
the file.
Commit: 89bafff06170c02e5089800a5062e3de0421ad23
https://github.com/galaxyproject/galaxy/commit/89bafff06170c02e5089800a5062…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tools/data_manager.py
Log Message:
-----------
Whitespace fix
Commit: c3886b373e8954c1f7bb193cf28357aebd8cd459
https://github.com/galaxyproject/galaxy/commit/c3886b373e8954c1f7bb193cf283…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/queue_worker.py
Log Message:
-----------
Specifically index new toolbox
Commit: 6fd4c5a5be75a39e941ab4b4b4df95c9456ca1e9
https://github.com/galaxyproject/galaxy/commit/6fd4c5a5be75a39e941ab4b4b4df…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Keep track of toolbox reload time
Commit: 230e7df4ae293e46e4f15bf2cf811f788a9f811d
https://github.com/galaxyproject/galaxy/commit/230e7df4ae293e46e4f15bf2cf81…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
Log Message:
-----------
Use cache to get the repository containing a tool
when reloading toolbox. This should prevent lots of (slow)
database requests when reloading the toolbox.
Commit: c5406eb192a0e2355602e5e5d7eb1e218a632d07
https://github.com/galaxyproject/galaxy/commit/c5406eb192a0e2355602e5e5d7eb…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Improve logic handling of loading tools
Commit: ab9be8c311a7943d778842522a706451e9996943
https://github.com/galaxyproject/galaxy/commit/ab9be8c311a7943d778842522a70…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fetch cached tools repository
Commit: 894b77ba23fa66a8852b554aacf18cc123f5d7cd
https://github.com/galaxyproject/galaxy/commit/894b77ba23fa66a8852b554aacf1…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/lineages/factory.py
Log Message:
-----------
Simplify lineage registration
Commit: acc5b4ceb6525a9cf53bf39c3d6c00abf9069990
https://github.com/galaxyproject/galaxy/commit/acc5b4ceb6525a9cf53bf39c3d6c…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
Log Message:
-----------
Load all versions in a single request
Commit: 971227c59dd1d32b537c04c59a16e7572aa7acbd
https://github.com/galaxyproject/galaxy/commit/971227c59dd1d32b537c04c59a16…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
A lib/galaxy/util/profiling.py
Log Message:
-----------
Use tool version cache to boost tool panel loading
Commit: 833af5e8c2121947e16bdfb99b2794b7a130d045
https://github.com/galaxyproject/galaxy/commit/833af5e8c2121947e16bdfb99b27…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/util/profiling.py
Log Message:
-----------
Restore peacemeal tool registration
Commit: 8bed867fcfcf249838b6b24a1b5985af401b9b5a
https://github.com/galaxyproject/galaxy/commit/8bed867fcfcf249838b6b24a1b59…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
Log Message:
-----------
Reload tool_version_cache after new installs
in the unit-testing code.
Commit: 894ac295207430d5ec1b02a0be7ee76ce4dc2cc0
https://github.com/galaxyproject/galaxy/commit/894ac295207430d5ec1b02a0be7e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/tool_shed/tools/tool_version_manager.py
Log Message:
-----------
Reload tool_version_cache when adding new tool
version relationships to the database.
Commit: 09173cc6070bc914759f15854367d62ca6323c79
https://github.com/galaxyproject/galaxy/commit/09173cc6070bc914759f15854367…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/util/profiling.py
M lib/tool_shed/tools/tool_version_manager.py
Log Message:
-----------
Rebase and linting fixes
Commit: d06e2a672b0c81e5391e077288bf36001f72dbb5
https://github.com/galaxyproject/galaxy/commit/d06e2a672b0c81e5391e077288bf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M tools/data_source/upload.xml
Log Message:
-----------
XSD discovered tool problems.
Commit: d98dcd75db307de955391c46e4121a0cd3036f3e
https://github.com/galaxyproject/galaxy/commit/d98dcd75db307de955391c46e412…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Merge pull request #2898 from jmchilton/fix_2806
Seemingly fix #2806.
Commit: c08db31ab22aefa23a0e6472c4f115cff537668f
https://github.com/galaxyproject/galaxy/commit/c08db31ab22aefa23a0e6472c4f1…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
R lib/galaxy/util/profiling.py
Log Message:
-----------
Document ToolVersionCache class
Commit: 92d028cbae55d120326cfac61f2fd4fb5d425b35
https://github.com/galaxyproject/galaxy/commit/92d028cbae55d120326cfac61f2f…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M test/unit/tools_support.py
Log Message:
-----------
Remove unnecessary self.install_model from unittest app
Commit: 0c3b5272eb53256b892a313aa6fcc4d5d5b5daa0
https://github.com/galaxyproject/galaxy/commit/0c3b5272eb53256b892a313aa6fc…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M tools/data_source/upload.xml
Log Message:
-----------
Merge pull request #2903 from jmchilton/format_fixes
XSD discovered tool problems.
Commit: 5c45da362ad27c788fe5f7e62fd5c779b7fa24bf
https://github.com/galaxyproject/galaxy/commit/5c45da362ad27c788fe5f7e62fd5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
Log Message:
-----------
Merge pull request #2901 from mvdbeek/fix_data_manager_hangs
All-around improvements to toolbox loading/reloading
Commit: 4df654d7da363afad10c7dc78a35a3f6c3a3d1bf
https://github.com/galaxyproject/galaxy/commit/4df654d7da363afad10c7dc78a35…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M .gitignore
Log Message:
-----------
Add `database/dependencies` gitignore
Since the galaxy.ini.sample file is shipped with `#tool_dependency_dir = database/dependencies` as default, and we don't want anyone commiting dependencies.
Commit: 14c0365b22d238e8c48b20dc64654cc412386059
https://github.com/galaxyproject/galaxy/commit/14c0365b22d238e8c48b20dc6465…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository revision
Commit: 9b414cd1fa2eb87187daff9677d5b0d552355009
https://github.com/galaxyproject/galaxy/commit/9b414cd1fa2eb87187daff9677d5…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M test/unit/tools_support.py
Log Message:
-----------
Minor fixes to shed tool lineage
get_installed_tool_version needs to look up the tool_version object
using the tool_id, not the tool_version id. Make sure toolshed tools in
cache have toolshed attribute.
Commit: 5e8a2ced3a819a238227bbde0627d90cfd3cf728
https://github.com/galaxyproject/galaxy/commit/5e8a2ced3a819a238227bbde0627…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/viewer.js
Log Message:
-----------
Distinguish draw and save to avoid accumulation of saved visualizations
Commit: cf9db96a1d7076474873c5b1f6e7ed2e32a3d79e
https://github.com/galaxyproject/galaxy/commit/cf9db96a1d7076474873c5b1f6e7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Change label from draw to visualize
Commit: a88942b0875f659e799d65bd00cea1d771c82570
https://github.com/galaxyproject/galaxy/commit/a88942b0875f659e799d65bd00ce…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/viewer.js
Log Message:
-----------
Unify labels and tooltips
Commit: 052b6e367bdeeffa5811853612a3bb1759c27039
https://github.com/galaxyproject/galaxy/commit/052b6e367bdeeffa5811853612a3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix tooltip
Commit: 48a841c0d9c80f03512314d31ac9f63358a186dc
https://github.com/galaxyproject/galaxy/commit/48a841c0d9c80f03512314d31ac9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M test/unit/tools_support.py
Log Message:
-----------
Merge pull request #2905 from mvdbeek/minor_lineage_bug
Minor fixes to shed tool lineage
Commit: c158d0b0611ed233b4b3d39fd23822e38d69d4db
https://github.com/galaxyproject/galaxy/commit/c158d0b0611ed233b4b3d39fd238…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
Log Message:
-----------
Refactor shed tool lineage registration
to avoid using tool.tool_shed_repository if possible, since this is a
property of the tool instance, which results in a database query. These
sequential queries slow down reloading a large number of tools.
Commit: 7cc1579c5908186d02aa04f9e72495530d63fe75
https://github.com/galaxyproject/galaxy/commit/7cc1579c5908186d02aa04f9e724…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-12 (Mon, 12 Sep 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
Log Message:
-----------
Merge pull request #2909 from mvdbeek/last_speed_fix
Refactor shed tool lineage registration
Commit: b102e2012342078a3b8bcab8348b2aaa485aa2a6
https://github.com/galaxyproject/galaxy/commit/b102e2012342078a3b8bcab8348b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-12 (Mon, 12 Sep 2016)
Changed paths:
M .gitignore
Log Message:
-----------
Merge pull request #2904 from nturaga/update_gitignore
Add `database/dependencies` gitignore
Commit: 85c1a8f2e2c7e4a93a9df7c8c2a0b8aff952774d
https://github.com/galaxyproject/galaxy/commit/85c1a8f2e2c7e4a93a9df7c8c2a0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-13 (Tue, 13 Sep 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
Log Message:
-----------
Log the resolved dependency type
Commit: 167286ad93bea7853eb6d95b6112bd04ff4fa20c
https://github.com/galaxyproject/galaxy/commit/167286ad93bea7853eb6d95b6112…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-13 (Tue, 13 Sep 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M templates/show_params.mako
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Track used dependencies in job metadata and expose with job info.
Commit: 04db0a2348e671ff0b80612d001bd62f69c2e32b
https://github.com/galaxyproject/galaxy/commit/04db0a2348e671ff0b80612d001b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-13 (Tue, 13 Sep 2016)
Changed paths:
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
Log Message:
-----------
Correct comment (thanks @martenson)
Commit: 63f758f9976b5e5810cae8648fa926d2d4855e5e
https://github.com/galaxyproject/galaxy/commit/63f758f9976b5e5810cae8648fa9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-13 (Tue, 13 Sep 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M templates/show_params.mako
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Merge pull request #2917 from mvdbeek/log_dependency_type
Log the resolved dependency type
Commit: 8b13f63f423800bf17e51a99231fa35099b58519
https://github.com/galaxyproject/galaxy/commit/8b13f63f423800bf17e51a99231f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-14 (Wed, 14 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .gitignore
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dockerfiles.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M setup.cfg
M templates/show_params.mako
M templates/webapps/galaxy/workflow/run.mako
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 921933ea9cb108a45f804f36adc0dc76d447ed11
https://github.com/galaxyproject/galaxy/commit/921933ea9cb108a45f804f36adc0…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-14 (Wed, 14 Sep 2016)
Changed paths:
M lib/galaxy/managers/rbac_secured.py
M test/unit/managers/test_DatasetManager.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into dev
Commit: 694fac5f567491471dadd11bb934dbec5746cafd
https://github.com/galaxyproject/galaxy/commit/694fac5f567491471dadd11bb934…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-14 (Wed, 14 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
-----------
Implement on random validator ``split``.
Commit: 7e8bee8830d5d82e222b350d4bc240d1206e5af3
https://github.com/galaxyproject/galaxy/commit/7e8bee8830d5d82e222b350d4bc2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A galaxy.xsd
Log Message:
-----------
Deleting directories from SVN that should have been ignored.
git-svn-id: https://svn.msi.umn.edu/tint/trunk@427 29e1c259-b37a-0410-ae23-5fb2df606144
Commit: 39fb238e666bb404b140b9ec37f1caeeb8a2637f
https://github.com/galaxyproject/galaxy/commit/39fb238e666bb404b140b9ec37f1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Work on galaxy support, implemented repeat blocks in the UI.
Commit: a718608e838f796bddb159b4e303194db52b3085
https://github.com/galaxyproject/galaxy/commit/a718608e838f796bddb159b4e303…
Author: Jean-Frédéric <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A README.md
Log Message:
-----------
Add basic ReadMe
Commit: 6e689fa77eef72020f62e00149bddfae825e299f
https://github.com/galaxyproject/galaxy/commit/6e689fa77eef72020f62e00149bd…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Remove custom namespaces
Commit: e1fc626fc1d6f2e49519784bea217ea3022d4073
https://github.com/galaxyproject/galaxy/commit/e1fc626fc1d6f2e49519784bea21…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Change tool element to <xs:all>
Element order is not enforced by Galaxy.
Commit: 025a22b0e7bbb8f9fc89dac33c8e18fdfc49b36f
https://github.com/galaxyproject/galaxy/commit/025a22b0e7bbb8f9fc89dac33c8e…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <requirements> tag set
This includes:
-<requirements>
-<requirement>
-Enumeration RequirementType
Commit: 08f1faad44fde20cf0748d7c12785300d67942ec
https://github.com/galaxyproject/galaxy/commit/08f1faad44fde20cf0748d7c1278…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Complete <repeat> tag set
Add attributes min and max to Repeat element
Commit: 9a9ba49caab8c63cff05153948160acccd80f912
https://github.com/galaxyproject/galaxy/commit/9a9ba49caab8c63cff0515394816…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <options> tag to <param>
The <param> tag can contain <options> to dynamically create a list of options.
Commit: 6b828d2b29b1612c82bcd7348625318628712aaf
https://github.com/galaxyproject/galaxy/commit/6b828d2b29b1612c82bcd7348625…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <label> tag to <param>
Commit: 150939e16a242a992d69bb771a6bf87f1936be40
https://github.com/galaxyproject/galaxy/commit/150939e16a242a992d69bb771a6b…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add missing attributes to <param> tag
Add seven missing attributes to <param> tag
Add the necessary datatypes for display, hierarchy and checked.
Commit: 62c32df6f1d7de93f04cd3a9b5fd7572f91f4363
https://github.com/galaxyproject/galaxy/commit/62c32df6f1d7de93f04cd3a9b5fd…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add missing attributes and element to <data> tag
Add three missing attributes to <data> tag
Add <filter> element to sequence
Commit: 73edfd6cf03c4366d4fd1036aa6fe3760958cd2a
https://github.com/galaxyproject/galaxy/commit/73edfd6cf03c4366d4fd1036aa6f…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Fix indentation
Commit: 91a166b7f5f42ee60495da20443b73d4bda1a502
https://github.com/galaxyproject/galaxy/commit/91a166b7f5f42ee60495da20443b…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <parallelism> tag
Add the <parallelism> tag (which serves for splitting job)
and the datatype for the 'method' attribute.
Commit: f9c5cf28ef2f60867a81dd8b6da3454e46d2936a
https://github.com/galaxyproject/galaxy/commit/f9c5cf28ef2f60867a81dd8b6da3…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <stdio> tag set to <tool>
Add <stdio> tag set, to handle tool messages on standard output
and standard error.
- Add <stdio> tag
- Add <regex> and <exit_code> sub elements
- Add datatypes for 'range', 'level' and 'source' attributes
Commit: 6e1d7e40a333d717a7c877c18eb94048dd99a7f0
https://github.com/galaxyproject/galaxy/commit/6e1d7e40a333d717a7c877c18eb9…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Change type for requirement version
Version information can be too complex for xs:decimal
(eg "0.12.7"). Change for xs:string.
Commit: 642e88857caa09d968f4e5c740dc44475a64e288
https://github.com/galaxyproject/galaxy/commit/642e88857caa09d968f4e5c740dc…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add column, filter and validator tags
Commit: 1787f1e89b4a311d9bae2c60effc851347da50e2
https://github.com/galaxyproject/galaxy/commit/1787f1e89b4a311d9bae2c60effc…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add ftype attribute to param tag in tests
Commit: 6181d24704fd23b3370a961ba3fb573d0100f099
https://github.com/galaxyproject/galaxy/commit/6181d24704fd23b3370a961ba3fb…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <code> tag set
Commit: 0da4d3c85361954a82fb8a0aa4c0f6bd742b9033
https://github.com/galaxyproject/galaxy/commit/0da4d3c85361954a82fb8a0aa4c0…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Remove required use from <requirement> version
Commit: 8164cfd3ba691dbb11fc5f623610b726ad5f2b85
https://github.com/galaxyproject/galaxy/commit/8164cfd3ba691dbb11fc5f623610…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Edit <options> tag set
Commit: bb285e4caee908cf4be30f0bf19ae21ffba20ebe
https://github.com/galaxyproject/galaxy/commit/bb285e4caee908cf4be30f0bf19a…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <validator> to <param>
Commit: 02aa90c4a477bb595540914df08ef9402275d84d
https://github.com/galaxyproject/galaxy/commit/02aa90c4a477bb595540914df08e…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add 'split' attribute to <validator>
Commit: e200148feef9ff553820272d7893b387e6e4723d
https://github.com/galaxyproject/galaxy/commit/e200148feef9ff553820272d7893…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <actions> tag set
Commit: 1c9513d6cb64315e742eab7befec7536dee766c8
https://github.com/galaxyproject/galaxy/commit/1c9513d6cb64315e742eab7befec…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Extend CheckedType to accept unspecified values
According to the documentation, CheckedType can either
be 'yes', 'true' or 'on' ; but many tools use '[Ff]alse'
which seems to be accepted/ignored by Galaxy.
Commit: b35b9fd52c78a891555660d7512e617b03d36cc0
https://github.com/galaxyproject/galaxy/commit/b35b9fd52c78a891555660d7512e…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add PermissiveBoolean datatype
<xs:boolean> can either be 'true', 'false', '1' or 'O' ; but many
Galaxy tools use 'True' and 'False' (capitalized), which appears
to be ignored/accepted by Galaxy.
This PermissiveBoolean type is meant to be used in place of xs:boolean
when needed.
Commit: dd0ba4293dc03db422a7b33e974c3b7554c287e9
https://github.com/galaxyproject/galaxy/commit/dd0ba4293dc03db422a7b33e974c…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add attributes 'ftype' and 'sort' to test <output>
These are undocumented attributes.
Commit: 4578e0a0f957ef7f851257b7bb605764712c5a44
https://github.com/galaxyproject/galaxy/commit/4578e0a0f957ef7f851257b7bb60…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) attributes to <filter>
Add attributes 'compare', 'keep' and 'value' to <filter> tag
(though these attributes are not documented).
Add CompareType for possible 'compare' values.
Commit: 4bdfd455c58d00c5a28fdf1e6fc80d70648cb57a
https://github.com/galaxyproject/galaxy/commit/4bdfd455c58d00c5a28fdf1e6fc8…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Edit filter tag for output tag
Commit: 566e279172c98e417c7fca9cf04bda2e3abd2da5
https://github.com/galaxyproject/galaxy/commit/566e279172c98e417c7fca9cf04b…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Rewrite <actions> handling
Commit: 1cda2e4439f28229d000f30120ecf69709606b6f
https://github.com/galaxyproject/galaxy/commit/1cda2e4439f28229d000f30120ec…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) 'dbkey' attribute to TestParam
Commit: 081c39e55161e1d1babebed1d159f2415a8e0adb
https://github.com/galaxyproject/galaxy/commit/081c39e55161e1d1babebed1d159…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add 'from_file' value to ActionsOptionType
Commit: b466de7e0a5e019d1a4264f2982f8c2012715241
https://github.com/galaxyproject/galaxy/commit/b466de7e0a5e019d1a4264f2982f…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Use PermissiveBoolean for ParamOption 'selected'
Commit: 92b1076261ee0403ff8fb6f8e2601ba5149e9807
https://github.com/galaxyproject/galaxy/commit/92b1076261ee0403ff8fb6f8e260…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add attributes tool_type and URL_method to <tool>
And corresponding enumeration Datatypes.
Commit: e8f236a52e5c4081ef9a228e15ffefb50185db7f
https://github.com/galaxyproject/galaxy/commit/e8f236a52e5c4081ef9a228e15ff…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
use PermissiveBoolean on two attributes of <param>
Commit: 7d7b5a8d3dfc604335626f0abf806377dc2b630c
https://github.com/galaxyproject/galaxy/commit/7d7b5a8d3dfc604335626f0abf80…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) value 'no' to CheckedType
Commit: e19f1fb99a982cedebc74a3b42f0c376e19d46bc
https://github.com/galaxyproject/galaxy/commit/e19f1fb99a982cedebc74a3b42f0…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) <uihints> to <tool>
See /lib/galaxy/tools/__init__.py:1069 for usage
Commit: 836aff4b3f70d6073bbd5f4d78d4b6688aed7baa
https://github.com/galaxyproject/galaxy/commit/836aff4b3f70d6073bbd5f4d78d4…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) attributes to <inputs>
Add attributes 'action', 'check_values', 'method' and 'target'
to <inputs>.
Add relevant Target datatype.
Commit: c4769e701302625031db4a7730e572b32c019ead
https://github.com/galaxyproject/galaxy/commit/c4769e701302625031db4a7730e5…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add <sanitizer> tag
Commit: 5419b1a4bce60a4459b59711acbf9c2652d5722d
https://github.com/galaxyproject/galaxy/commit/5419b1a4bce60a4459b59711acbf…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) attribute metadata_name to <param>
Commit: 79cf1c57d8b6a1add066bf61ec18936bf1a8f6ee
https://github.com/galaxyproject/galaxy/commit/79cf1c57d8b6a1add066bf61ec18…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) attributes to <options>
Add 'options_filter_attribute' attribute
(see lib/galaxy/tools/parameters/basic.py)
Add 'transform_lines' attribute
(see lib/galaxy/tools/parameters/dynamic_options.py)
transform_lines and
Commit: 11b013f402b90c742789df87b6810e156a173171
https://github.com/galaxyproject/galaxy/commit/11b013f402b90c742789df87b681…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) 'ref_attribute' to <filter>
Add attribute 'ref_attribute' to <filter>
(see lib/galaxy/tools/parameters/dynamic_options.py:153)
Commit: 65903327fa21536d44822ef94a9e75b2d29cf11d
https://github.com/galaxyproject/galaxy/commit/65903327fa21536d44822ef94a9e…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) 'startswith' to <options>
Add attribute 'startswith' to <options> tag
(see lib/galaxy/tools/parameters/dynamic_options.py:416)
Commit: d12766e260ea8d1e6ebe61806cb7e2b3eb55b886
https://github.com/galaxyproject/galaxy/commit/d12766e260ea8d1e6ebe61806cb7…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Add (undocumented) attribute 'display' to <inputs>
See lib/galaxy/tools/__init__.py:1531
Commit: 091b3b85687eeb8ef5becdf30ff81211b12f6f45
https://github.com/galaxyproject/galaxy/commit/091b3b85687eeb8ef5becdf30ff8…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Fix value baseurl in <param> 'type' attribute
Commit: 395780d3d143982204c1f9ccf188df1deff51d55
https://github.com/galaxyproject/galaxy/commit/395780d3d143982204c1f9ccf188…
Author: JeanFred <jean-frederic.berthelot(a)lifl.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Fix type of min and max in <validator>
Commit: 2fdf2267b841d2701db424f9d2f458d8fbc2309b
https://github.com/galaxyproject/galaxy/commit/2fdf2267b841d2701db424f9d2f4…
Author: Pierre Lindenbaum <plindenbaum(a)yahoo.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A .gitignore
A Makefile
M README.md
A citation.xsd
A citations.xsd
A galaxy.jxb
M galaxy.xsd
A test.urls
Log Message:
-----------
added doc and JXB bindings
Commit: 2cecbe1922a9b5d75f34d42bedcd025a83fbae09
https://github.com/galaxyproject/galaxy/commit/2cecbe1922a9b5d75f34d42bedcd…
Author: Pierre Lindenbaum <plindenbaum(a)yahoo.fr>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M README.md
Log Message:
-----------
updated README
Commit: f692d3a5ae244ce638be596723f369dade3ed501
https://github.com/galaxyproject/galaxy/commit/f692d3a5ae244ce638be596723f3…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A .travis.yml
Log Message:
-----------
Add Continuous integration with Travis for XSD linting
At the very least these XSD files should be XML valid.
Commit: cdbe79b4b657609724081c991466b0be13460d36
https://github.com/galaxyproject/galaxy/commit/cdbe79b4b657609724081c991466…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M .travis.yml
Log Message:
-----------
Fix dependency installation for Travis
Build was failing with
$ apt-get install libxml2-utils
E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied)
E: Unable to lock the administration directory (/var/lib/dpkg/), are you root?
APT dependencies must be installed as sudoer.
Commit: 00a560ce1dbb093989b36f628abf08bf5ad3ee91
https://github.com/galaxyproject/galaxy/commit/00a560ce1dbb093989b36f628abf…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M README.md
Log Message:
-----------
Add Travis badge to ReadMe
Commit: 3315e9a8c424281df01e7521a9c9715447356059
https://github.com/galaxyproject/galaxy/commit/3315e9a8c424281df01e7521a9c9…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A test.sh
Log Message:
-----------
Add Shell test script
Following the idea of @lindenb in the Makefile.
This tests all the given URLs in test.urls and
outputs a compliant TAP.
Commit: bcc20e289fc9c4df1615530b264a6cada2e39974
https://github.com/galaxyproject/galaxy/commit/bcc20e289fc9c4df1615530b264a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M README.md
Log Message:
-----------
Add me (@jmchilton) to authors list.
My name is on the earliest commits (thanks for preserving that).
Commit: 1b7f2a54f6c2b12d9340fe4c8c3e8de0f0f68afb
https://github.com/galaxyproject/galaxy/commit/1b7f2a54f6c2b12d9340fe4c8c3e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M citation.xsd
M test.urls
Log Message:
-----------
Fix CitationType attribute.
Add Galaxy's test tool for citations to test.urls.
Commit: 057c36997bd5c4c75a85acd5a9346f8c28eee015
https://github.com/galaxyproject/galaxy/commit/057c36997bd5c4c75a85acd5a934…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
M test.urls
Log Message:
-----------
Update XSD for container tags.
Add Galaxy test tool for Docker container tags to test.urls.
Commit: bdf36556fbf4c4db4c343e51d6d78c1ac2030464
https://github.com/galaxyproject/galaxy/commit/bdf36556fbf4c4db4c343e51d6d7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Drop embeddedValue for test stuff.
These were an extension to the Galaxy XML syntax for TINT - which is no longer actively maintained.
Commit: f0799b5fbb9dfe54241b702c450f258c946bf326
https://github.com/galaxyproject/galaxy/commit/f0799b5fbb9dfe54241b702c450f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
M test.urls
Log Message:
-----------
Start work on implementing assert_contents tag in tests.
Just enough to get Galaxy's simple_contructrs.xml to validate - add this to test.urls. More work should be done on these - but it should be automated derived from Galaxy somehow.
Commit: b479b7334fc6649606c5144da7c9225c82857e6b
https://github.com/galaxyproject/galaxy/commit/b479b7334fc6649606c5144da7c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
M test.urls
Log Message:
-----------
Update XSD for very basic data collection usage.
- Allow 'data_collection' parameters and allow them to specify a 'collection_type'.
- Allow test parameters to be flat collections.
- Add test/functional/tools/collection_paired_test.xml to test.urls to check all of this.
Lots more TODO for recent tool collection support - output collections definitions, output collection tests, dynamic discovery tags, specifying nested collections for test inputs.
Commit: 49f7d51f57eb2f72e01e37fdaf6c44ffe11898de
https://github.com/galaxyproject/galaxy/commit/49f7d51f57eb2f72e01e37fdaf6c…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A LICENSE
M README.md
Log Message:
-----------
Add MIT license
Per agreement of all authors.
Closes #2.
Commit: 8947f29ef2596e750d2783206df547efc7ef40fd
https://github.com/galaxyproject/galaxy/commit/8947f29ef2596e750d2783206df5…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M README.md
Log Message:
-----------
Expand history in ReadMe
Commit: 5d40c7b3e2b66d91a52ae12cf48cda30d245d180
https://github.com/galaxyproject/galaxy/commit/5d40c7b3e2b66d91a52ae12cf48c…
Author: Jean-Fred <JeanFred@github>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M LICENSE
Log Message:
-----------
Fix authors in License file
Follow up on #2.
Commit: a4e5568af7f206c61ebf7afd9165bd1e34181d0b
https://github.com/galaxyproject/galaxy/commit/a4e5568af7f206c61ebf7afd9165…
Author: Michael R. Crusoe <crusoe(a)ucdavis.edu>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
first try
Commit: 8f8cc890bcfaceaf4870daa2d4e22e10018119c2
https://github.com/galaxyproject/galaxy/commit/8f8cc890bcfaceaf4870daa2d4e2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Improvements to XSD:
- Implement section.
- Implement and document request_parameter_translation, request_parameter and its children (value_translation and append_param).
- Implement detect_errors on the command block and document defaults.
Commit: 63c019b13b44fedc9159909eb7995294d3653244
https://github.com/galaxyproject/galaxy/commit/63c019b13b44fedc9159909eb799…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More progress...
- Fix to previous commit.
- Remove downstream config file type that was abandoned work and not in galaxy-core.
- More documentation for configfile stuff.
- Improvements to representation for output and santizer.
Commit: 1125f1b8ea8b993ac5493f663b76c4ba54350ee4
https://github.com/galaxyproject/galaxy/commit/1125f1b8ea8b993ac5493f663b76…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Simplify schema and improve docs related to sanitization.
Commit: 21cd752e252d17fdba2401cbe78bc3ef62ffd327
https://github.com/galaxyproject/galaxy/commit/21cd752e252d17fdba2401cbe78b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Improve docs on filter and change_format of outputs.
Commit: 804c072d5af2e5704d57a503a84ad6733f03c1c0
https://github.com/galaxyproject/galaxy/commit/804c072d5af2e5704d57a503a84a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
And more progress...
- Docs for help.
- Docs for tests.
- Docs for code files.
- Implementing more of the assert_xxx test flags.
- Improved coverage of test assertion element descriptions.
Commit: 23449750d46e4df208fc46d1c2a4d3840cd080f4
https://github.com/galaxyproject/galaxy/commit/23449750d46e4df208fc46d1c2a4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More progress...
- Refine test outputs and include syntax for testing extra files and md5sums.
Commit: 3d3c3fee4f576408c223c723b57b003ae6ccf4c1
https://github.com/galaxyproject/galaxy/commit/3d3c3fee4f576408c223c723b57b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More progress.
- Add strict to command.
- Add conditional and repeat to test params.
- Add count to output collections.
- Implement more collection output attributes (type_source, etc...).
- Reduce need for type on collection defs (since type_source can be defined).
Commit: 80d086b861f1401568b967d96e2e37461ca677a2
https://github.com/galaxyproject/galaxy/commit/80d086b861f1401568b967d96e2e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More progress...
- Allow section in test parameters.
- Implement basic metadata testing.
Commit: 19b273cdf55df6b2593715d7daaf4690d8d6935b
https://github.com/galaxyproject/galaxy/commit/19b273cdf55df6b2593715d7daaf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More progress...
- Allow nested elements in test output collections (hackily)
- Implement ``compare`` and ``delta`` for test output comparison.
- Implement the new ``checksum`` output test.
Commit: 7f5cc04c114bd5e696e7e54697e5a7bf58277fa7
https://github.com/galaxyproject/galaxy/commit/7f5cc04c114bd5e696e7e54697e5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More progress...
- Add tool action.
- Stub workflow_compatible and profile_version attributes on tool.
- Add many more attributes to parallelism tag.
- Add maxseconds and expect_num_outputs to tool test tag.
- Small fix to <repeat> block in test cases.
- Implement assigning metadata in test params.
- Allow more versitle ordering of test blocks (too permissive now).
- Implement testing of output metadata and discovered datasets.
- Add nginx_upload attribute used by upload.xml and various conditional attributes for pulling in values from Galaxy internals.
- Implement the stub of a ``upload_dataset`` param and say not to use it.
- Add color and library data parameter types.
- More attributes to filters and validators.
- Implement auto_format on outputs.
- Implement filters and explicit data outputs on output collections.
- Implement inputs as json element.
- Add empty dataset validator.
Commit: 49ff357854ff1a8dab9d792c0d97881f33c5a603
https://github.com/galaxyproject/galaxy/commit/49ff357854ff1a8dab9d792c0d97…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Stub out environment variables and add a new tool type.
Commit: c6ae6ee8cb3c240923e4738f0e8f0a4a1134cbd5
https://github.com/galaxyproject/galaxy/commit/c6ae6ee8cb3c240923e4738f0e8f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
R citation.xsd
R citations.xsd
M galaxy.xsd
Log Message:
-----------
Embed citations right in galaxy.xsd.
Not that I mind splitting it up - but it will make a couple things easier downstream and those few tags weren't enough to warrent breaking things up like that.
Commit: dcfdd3ceaa62ccee0a8d22c6d299eab2742df47f
https://github.com/galaxyproject/galaxy/commit/dcfdd3ceaa62ccee0a8d22c6d299…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Many more fixes derived from testing tools-iuc.
Commit: 8c2a4e12758827b0855181de962ef0f0a61515a7
https://github.com/galaxyproject/galaxy/commit/8c2a4e12758827b0855181de962e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
And more progress - now covers all Galaxy test tools and all IUC.
- Add <options> block.
- Add <trackster_conf> block.
- Add a newerish validator and allow filter/validator columns to be column names.
- More permissives boolean values to match Galaxy in various places.
- Other mostly obsecure features.
Commit: ff6cca8635e6ce1c906dd316dcc0d6ab0bed7fb3
https://github.com/galaxyproject/galaxy/commit/ff6cca8635e6ce1c906dd316dcc0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Doc updates
Commit: 491efe8c4951eedecc1635dbc972fb49ec883230
https://github.com/galaxyproject/galaxy/commit/491efe8c4951eedecc1635dbc972…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Doc improvements.
Commit: 94ad78da97b98eee05a5ff0f890eec0e518845b7
https://github.com/galaxyproject/galaxy/commit/94ad78da97b98eee05a5ff0f890e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Much richer documentation for a few tags including ``command``.
Commit: e9f08b411a0bf4ef8620bc66fb7c10d61112fb49
https://github.com/galaxyproject/galaxy/commit/e9f08b411a0bf4ef8620bc66fb7c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
More work on documentation - revise last commit and add repeats and sections.
Commit: 2e31bc932dd9bd96d403cd8e6ef20715785c3eef
https://github.com/galaxyproject/galaxy/commit/2e31bc932dd9bd96d403cd8e6ef2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Work on docs.
Commit: 8f2f62a75a7aa256904821888c09682ebde99c83
https://github.com/galaxyproject/galaxy/commit/8f2f62a75a7aa256904821888c09…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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More docs...
- Added docs for param's option.
- Started work on validators and options, but are WIP though.
Commit: 4bcfe568b713e9369d0d1e5090e140d7ebfee17c
https://github.com/galaxyproject/galaxy/commit/4bcfe568b713e9369d0d1e5090e1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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More docs for validators.
Commit: 2980835dc7ec8b2ba2e1cde39142e0697c4fc9f8
https://github.com/galaxyproject/galaxy/commit/2980835dc7ec8b2ba2e1cde39142…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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A lot more documentation around parameter options.
Also fixed a bit of a problem - turns out <filter> in action conditionals is very different than filter in options so I've split these types out.
Commit: cd5328dce2aff381df95fa7b523dc40bc525f704
https://github.com/galaxyproject/galaxy/commit/cd5328dce2aff381df95fa7b523d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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More documentation...
Cleaned up the stdio tags and help section, flushed out citations and parameter options. Small touchups other places also.
Commit: 24f46245e09ef044cca6804c48c994e49b70b69a
https://github.com/galaxyproject/galaxy/commit/24f46245e09ef044cca6804c48c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Mention code files as a way to generate dynamic options.
Transplant example from Galaxy wiki of doing this.
Commit: 6481a00f88bff4bb7a7adbf2aaaee639e4649147
https://github.com/galaxyproject/galaxy/commit/6481a00f88bff4bb7a7adbf2aaae…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Flush out docs for requirements and child tags.
Commit: 3af76de52ff56fca6b65d993ce91fb39c30af2d2
https://github.com/galaxyproject/galaxy/commit/3af76de52ff56fca6b65d993ce91…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Flush out docs for sanitizers, configfiles, etc...
Commit: b059c8b592b0f45dd669f8e9cbca714ed292ccac
https://github.com/galaxyproject/galaxy/commit/b059c8b592b0f45dd669f8e9cbca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Working my way through basic parameter documentation.
Commit: 366def7026a68e2bde75a140e3e4f1496966b1f2
https://github.com/galaxyproject/galaxy/commit/366def7026a68e2bde75a140e3e4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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More work on parameters and environment variables.
Commit: 4ba421e2f67de03dfa51ad8493f9a27beb159f27
https://github.com/galaxyproject/galaxy/commit/4ba421e2f67de03dfa51ad8493f9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Finishing first pass at filling out wiki docs for ``param``.
And other small fixes.
Commit: 5ad6e790e2f1a752beb748581469aa2e9f73477f
https://github.com/galaxyproject/galaxy/commit/5ad6e790e2f1a752beb748581469…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Starting to polish and flush out data outputs documentation.
Commit: e2d55ccf1685ec767d2c09715b189c7a1ff411cb
https://github.com/galaxyproject/galaxy/commit/e2d55ccf1685ec767d2c09715b18…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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More docs - conditional output actions and some more on discover datasets.
Commit: 89c8934727c7a8b8cc4ca7db10e7882d22542a87
https://github.com/galaxyproject/galaxy/commit/89c8934727c7a8b8cc4ca7db10e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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A bunch of work on cleaning up and flushing out documentation for test tags.
Commit: c607727d83c079a2859ed9026d26edbb52f4bcf9
https://github.com/galaxyproject/galaxy/commit/c607727d83c079a2859ed9026d26…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Document the test ``output_collection`` tag.
Commit: fc440a87c4883a9244d5e45783e2f27b639319cb
https://github.com/galaxyproject/galaxy/commit/fc440a87c4883a9244d5e45783e2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Fix missing annotation.
Commit: 60def6204d1ba2299442a76856f19ab53ffe1e92
https://github.com/galaxyproject/galaxy/commit/60def6204d1ba2299442a76856f1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Fixes of structure broken with docs.
Commit: b74c1a5b0baa6da94ca45f11a1e8e2057fcf2790
https://github.com/galaxyproject/galaxy/commit/b74c1a5b0baa6da94ca45f11a1e8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Use the new action conditional filter.
Commit: 195fd46604a64ad8928ead83d6cd6f7f51a2639c
https://github.com/galaxyproject/galaxy/commit/195fd46604a64ad8928ead83d6cd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Add a fictious XML schema with Galaxy stuff.
New attributes:
- deprecated
- best_practices (provides links of the form http://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_…)
Commit: 4dd8da09b8bd1917094622039adfe01cffa2fd40
https://github.com/galaxyproject/galaxy/commit/4dd8da09b8bd1917094622039adf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Remove embedded best practice stuff - the help will have links now.
Commit: c4f03079d7fefb2e37790b4d07fe7d0a67990d8d
https://github.com/galaxyproject/galaxy/commit/c4f03079d7fefb2e37790b4d07fe…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Fill out some docs for test sections...
Commit: 0c6be2095710fbb79bd9b9fdd231e960bb9f2ce8
https://github.com/galaxyproject/galaxy/commit/0c6be2095710fbb79bd9b9fdd231…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M test.sh
Log Message:
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Revise automated testing, check against test tools and IUC tools.
Commit: b9d25b848c333226e503d4f301187a43dbebc584
https://github.com/galaxyproject/galaxy/commit/b9d25b848c333226e503d4f30118…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Document testing discovered datasets and metadata.
Commit: 8b7ae4bc7b446b0b00758f6cf0c98e7eaece96ce
https://github.com/galaxyproject/galaxy/commit/8b7ae4bc7b446b0b00758f6cf0c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
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Fix a syntax error.
Commit: 236bdf5a40d0d720a72b7c71b03e2cb79fc576d4
https://github.com/galaxyproject/galaxy/commit/236bdf5a40d0d720a72b7c71b03e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M galaxy.xsd
Log Message:
-----------
Update the link for multiple outputs.
Commit: 3d7ae4e38fea3d7f84368ccb57f107f0c13f9749
https://github.com/galaxyproject/galaxy/commit/3d7ae4e38fea3d7f84368ccb57f1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
R .gitignore
R .travis.yml
R LICENSE
R Makefile
R README.md
R galaxy.jxb
R galaxy.xsd
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/Makefile
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
A lib/galaxy/tools/xsd/test.sh
A lib/galaxy/tools/xsd/test.urls
R test.sh
R test.urls
Log Message:
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Relocate Galaxy XSD files into Galaxy directory structure.
Commit: 491c9fd519be37b6c6f57cd4082d981c9f411ba5
https://github.com/galaxyproject/galaxy/commit/491c9fd519be37b6c6f57cd4082d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
R lib/galaxy/tools/xsd/Makefile
R lib/galaxy/tools/xsd/test.urls
Log Message:
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Cleanup XSD for move to Galaxy core.
Commit: c4d8dddc5cbfe416e5931e409db9e63804688f1e
https://github.com/galaxyproject/galaxy/commit/c4d8dddc5cbfe416e5931e409db9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
A lib/galaxy/tools/xsd/test.sh
Log Message:
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Merge branch 'master' of Galaxy-XSD into 'dev'
Commit: babaf7a2c675648e2851f81d985a72321b4eeb44
https://github.com/galaxyproject/galaxy/commit/babaf7a2c675648e2851f81d985a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
R lib/galaxy/tools/xsd/test.sh
Log Message:
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Address reviewer comments on XSD.
- Merge in @bgruening's numerous awesome fixes.
- Remove test script with issues that make if not a fit for this repo in that form (noted by @nsoranzo).
- Incorporate other changes to the XSD suggested by @nsoranzo.
Commit: f553d387a47d0ef1a58a1522c0f437e3b1783a59
https://github.com/galaxyproject/galaxy/commit/f553d387a47d0ef1a58a1522c0f4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
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Merge pull request #2880 from jgoecks/bbi-js3
Trackster: Read numerical data directly from bigwig files
Commit: e76bbf53b62f29f2d05459ecea13fd8e98449aa4
https://github.com/galaxyproject/galaxy/commit/e76bbf53b62f29f2d05459ecea13…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
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Merge pull request #2885 from carlfeberhard/file-walker
API, history contents: contents download endpoint
Commit: 70251b5b6a8363a627fccf90f642c3a02cc57cd5
https://github.com/galaxyproject/galaxy/commit/70251b5b6a8363a627fccf90f642…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/LICENSE
Log Message:
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Update the LICENSE for the XSD file.
Commit: a698fa52b3aef236cbf6bad729e286552b84114c
https://github.com/galaxyproject/galaxy/commit/a698fa52b3aef236cbf6bad729e2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M LICENSE.txt
Log Message:
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Update the Copyright year in the LICENSE.txt.
Commit: 9d24d55cb5e515b8e8f9654e070ae17aae864367
https://github.com/galaxyproject/galaxy/commit/9d24d55cb5e515b8e8f9654e070a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M CONTRIBUTORS.md
Log Message:
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Add XSD contributors to CONTRIBUTORS.md.
Commit: c576f27d4fba92c1066964fc1b32d24921a65771
https://github.com/galaxyproject/galaxy/commit/c576f27d4fba92c1066964fc1b32…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M LICENSE.txt
Log Message:
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Merge pull request #2926 from jmchilton/copyright
Update the Copyright year in the LICENSE.txt.
Commit: f34ab79d22b261e6606ae994f7c2b8bb14273ca2
https://github.com/galaxyproject/galaxy/commit/f34ab79d22b261e6606ae994f7c2…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/validation.py
Log Message:
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Merge pull request #2921 from jmchilton/implement_split
Implement ``split`` on a validator.
Commit: 4c60b812030423f7e4c755f7cbc57c83083ea834
https://github.com/galaxyproject/galaxy/commit/4c60b812030423f7e4c755f7cbc5…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
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Merge branch 'release_16.07' into dev
Conflicts:
lib/galaxy/tools/deps/__init__.py
Commit: 7a8d9af16b97677656234c68d88c760495b4d322
https://github.com/galaxyproject/galaxy/commit/7a8d9af16b97677656234c68d88c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
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Catch failure to import grp in util (for Pulsar on Windows)
Commit: 31b4eb155fa8f9f9d13d17ed60592f9cd99f23db
https://github.com/galaxyproject/galaxy/commit/31b4eb155fa8f9f9d13d17ed6059…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
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Merge pull request #2928 from natefoo/windows-util-fix
Catch failure to import grp in util (for Pulsar on Windows)
Commit: f12723dc8311b35c9cf7271dc3bc46f640bde00b
https://github.com/galaxyproject/galaxy/commit/f12723dc8311b35c9cf7271dc3bc…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M CONTRIBUTORS.md
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
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Merge pull request #2923 from jmchilton/merge_xsd_into_core
Merge Galaxy-XSD into project
Commit: bbf72ef932f7e7ef314b905e17b4958180f4eb11
https://github.com/galaxyproject/galaxy/commit/bbf72ef932f7e7ef314b905e17b4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
A .ci/validate_test_tools.sh
M .travis.yml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M tox.ini
Log Message:
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CI testing of newly integrated tool schema (XSD).
- Add CI script that lints the XSD definition and then validates all test tools against it.
- Add tox environment to run the aforementioned script.
- Add Travis check through tox to run the script.
- Drop the multi_page.xml test tool - pages have been removed from the framework and are not part of the schema (xref https://github.com/galaxyproject/galaxy/issues/1776).
This will hopefully ensure that all new tool features get added to the schema (as long as there is a test tool for the feature). xref https://github.com/galaxyproject/galaxy/pull/2923https://github.com/galaxyproject/galaxy/pull/2903
Largely based on work done in Galaxy-XSD by JeanFred (e.g. https://github.com/galaxyproject/Galaxy-XSD/commit/386ba087881877093d4be1f6…)
Commit: 05ae9959078a94da25a16ed8ef13f2a2d6aceb45
https://github.com/galaxyproject/galaxy/commit/05ae9959078a94da25a16ed8ef13…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M .ci/validate_test_tools.sh
A scripts/validate_tools.sh
Log Message:
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Refactor most of tool validation for CI into a standalone script.
Commit: 8ca517dc8b937e5f435e2a5046e3ecc32c27d504
https://github.com/galaxyproject/galaxy/commit/8ca517dc8b937e5f435e2a5046e3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M .travis.yml
M tox.ini
Log Message:
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More fixes pointed out by @nsoranzo for validation CI.
Commit: a58d50e14f31c0639069959ef4d68b75ef331580
https://github.com/galaxyproject/galaxy/commit/a58d50e14f31c0639069959ef4d6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
M .travis.yml
Log Message:
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Another fix thanks to @nsoranzo.
Commit: 71cea6604d43c5fe6215f5656462ba6c1af69bb6
https://github.com/galaxyproject/galaxy/commit/71cea6604d43c5fe6215f5656462…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-09-16 (Fri, 16 Sep 2016)
Changed paths:
A .ci/validate_test_tools.sh
M .travis.yml
A scripts/validate_tools.sh
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M tox.ini
Log Message:
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Merge pull request #2932 from jmchilton/validate_test_tools
CI testing of newly integrated tool schema (XSD).
Commit: b58b83e56e458efd749fb9966cfe087cfbf41c3d
https://github.com/galaxyproject/galaxy/commit/b58b83e56e458efd749fb9966cfe…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-19 (Mon, 19 Sep 2016)
Changed paths:
M lib/galaxy/web/framework/decorators.py
Log Message:
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Allow JSONP in api calls
Commit: ffd0ac78cd3920768ed84f6ab780c13d69532a45
https://github.com/galaxyproject/galaxy/commit/ffd0ac78cd3920768ed84f6ab780…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-19 (Mon, 19 Sep 2016)
Changed paths:
M lib/galaxy/web/framework/decorators.py
Log Message:
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Extend JSONP to older decorators
Commit: c69a20f76109754c846ac2d42e22ce87cdc96bca
https://github.com/galaxyproject/galaxy/commit/c69a20f76109754c846ac2d42e22…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/web/framework/decorators.py
Log Message:
-----------
API, jsonp: better var name
Commit: a312ef29e113f510d7fffa0343824b4491206c0a
https://github.com/galaxyproject/galaxy/commit/a312ef29e113f510d7fffa034382…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/web/framework/decorators.py
Log Message:
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API, jsonp: switch off for certain decorators
Commit: 35d0fed80145c7d07c0512ebcb9b4a23c4293072
https://github.com/galaxyproject/galaxy/commit/35d0fed80145c7d07c0512ebcb9b…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
Log Message:
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Merge branch 'release_16.07' into dev
Commit: 97532515ea24325ba26877696991b24401733ee6
https://github.com/galaxyproject/galaxy/commit/97532515ea24325ba26877696991…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/genomes.py
Log Message:
-----------
API access to genome fasta index and sequence
Allows visualization components, e.g. IGV.js, to incrementally retrieve sequence as needed.
Commit: 9ae56b782a241c373d3ef4496d9110763b31c951
https://github.com/galaxyproject/galaxy/commit/9ae56b782a241c373d3ef4496d91…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/web/framework/decorators.py
Log Message:
-----------
Merge pull request #2937 from carlfeberhard/jsonp
Allow JSONP to be returned from API endpoints
Commit: 10b310b87142a9f34a1ce5340575d6c351a2279b
https://github.com/galaxyproject/galaxy/commit/10b310b87142a9f34a1ce5340575…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/extract.py
M templates/webapps/galaxy/workflow/build_from_current_history.mako
Log Message:
-----------
Allow naming Dataset/collection inputs during workflow extraction. Default name is now the original input dataset name.
Commit: 9890cb63f12d2d2e5eccd40e931c5563732efd44
https://github.com/galaxyproject/galaxy/commit/9890cb63f12d2d2e5eccd40e931c…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M templates/webapps/galaxy/workflow/build_from_current_history.mako
Log Message:
-----------
Text inputs can't be checked.
Commit: 36b514c6e963b44b27003e7f64f0a9fe019f305e
https://github.com/galaxyproject/galaxy/commit/36b514c6e963b44b27003e7f64f0…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/util/checkers.py
Log Message:
-----------
Remove unnecessary use of binascii
Also explicitly specify binary mode for file opening and header strings.
Fix import order.
Commit: a8bc9d5d16244badb023a9c5097efd826b26db56
https://github.com/galaxyproject/galaxy/commit/a8bc9d5d16244badb023a9c5097e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M .gitignore
M Makefile
A doc/parse_gx_xsd.py
A doc/schema_template.md
Log Message:
-----------
XSD Generated Tool Documentation.
- Add script to generate Markdown documentation from the XSD.
- Add Makefile target to build these docs, convert to HTML, and open respectively.
Commit: 0e0b773edc85c3e36ae25f38ee929e8a95cc520b
https://github.com/galaxyproject/galaxy/commit/0e0b773edc85c3e36ae25f38ee92…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/security/validate_user_input.py
M templates/user/info.mako
M templates/user/register.mako
M test/unit/managers/test_UserManager.py
Log Message:
-----------
Allow '.' and '_' for public names
Fix #2593.
Also standardise error messages.
Commit: 70db2b7c4ad253b3ce0443d66df3832e4fc2a189
https://github.com/galaxyproject/galaxy/commit/70db2b7c4ad253b3ce0443d66df3…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Validate public name when auto-registering a user
Commit: 8fb3cd9c5bc52495e6055c0a2a5bb4339e31612b
https://github.com/galaxyproject/galaxy/commit/8fb3cd9c5bc52495e6055c0a2a5b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
Log Message:
-----------
propagate allowed changes to hints
Commit: 736df5a0717089f815e0ba02ef7e9502fef36814
https://github.com/galaxyproject/galaxy/commit/736df5a0717089f815e0ba02ef7e…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
Log Message:
-----------
Merge pull request #4 from martenson/nsoranzo-publicnames
propagate allowed username changes to form hints
Commit: f799656b1117d74afac0cd0c4ad1ca19625ca625
https://github.com/galaxyproject/galaxy/commit/f799656b1117d74afac0cd0c4ad1…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M test/unit/managers/test_UserManager.py
Log Message:
-----------
Merge pull request #2947 from nsoranzo/publicnames
Allow '.' and '_' for public names
Commit: 7d76bfe046fef24e25d4d04ef68b8228971aa79c
https://github.com/galaxyproject/galaxy/commit/7d76bfe046fef24e25d4d04ef68b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/extract.py
M templates/webapps/galaxy/workflow/build_from_current_history.mako
Log Message:
-----------
Merge pull request #2943 from blankenberg/wf_input_name
Allow naming Dataset/collection inputs during workflow extraction.
Commit: b30d331a811f2c5621ba81ff5bd54dc4ee93d755
https://github.com/galaxyproject/galaxy/commit/b30d331a811f2c5621ba81ff5bd5…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/jobs/runners/slurm.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Commit: c81ec07c6d39f7dbb080f0db3680d6a29747608a
https://github.com/galaxyproject/galaxy/commit/c81ec07c6d39f7dbb080f0db3680…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/util/checkers.py
Log Message:
-----------
Merge pull request #2946 from nsoranzo/binascii_reduction
Remove unnecessary use of binascii
Commit: 9c43103630eb8bceb10021b282b8296218c04729
https://github.com/galaxyproject/galaxy/commit/9c43103630eb8bceb10021b282b8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Remove html builders for tool parameters, strip run workflow mako
Commit: cd93da35c11f9374c5ffd03a44cbf33876dffb29
https://github.com/galaxyproject/galaxy/commit/cd93da35c11f9374c5ffd03a44cb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
R templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
Remove old run controller
Commit: 289ac4845ad79cc7ee2079784d31182d3df23027
https://github.com/galaxyproject/galaxy/commit/289ac4845ad79cc7ee2079784d31…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove unused checked list state for booleans
Commit: 9f6a88a28f968a03301e8a516f10a5322bc77f4e
https://github.com/galaxyproject/galaxy/commit/9f6a88a28f968a03301e8a516f10…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove unused to_dict parameters
Commit: cd91e3141c7d031b092091ce22345d87b8aa76d2
https://github.com/galaxyproject/galaxy/commit/cd91e3141c7d031b092091ce2234…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Rename regex parameter, fix spacing
Commit: b38b9fe2e1663d724651a0c6e1aa78e87acaa43d
https://github.com/galaxyproject/galaxy/commit/b38b9fe2e1663d724651a0c6e1aa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove comment
Commit: 13f498568c505b24f1b9753aaf158be324542219
https://github.com/galaxyproject/galaxy/commit/13f498568c505b24f1b9753aaf15…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove unused repeat handling
Commit: d5ca00d6892874dc7da54be0a45da3cea4acb878
https://github.com/galaxyproject/galaxy/commit/d5ca00d6892874dc7da54be0a45d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Adjust first half of test cases in basic paramter handling
Commit: 143a3ecffcc8da4469245b40336901f944b531e0
https://github.com/galaxyproject/galaxy/commit/143a3ecffcc8da4469245b403369…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix test cases
Commit: adfaa948e9f65c07bf8cf8a67791bb3dd0e30bc6
https://github.com/galaxyproject/galaxy/commit/adfaa948e9f65c07bf8cf8a67791…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Remove unused imports
Commit: c61933d1b1c0289735945bf97bf8b1f4bf5e5fc8
https://github.com/galaxyproject/galaxy/commit/c61933d1b1c0289735945bf97bf8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M test/unit/tools/test_data_parameters.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Fix dataset parameter tests
Commit: 979bdd44c60d5aab27e472b19afa8dd704ee195a
https://github.com/galaxyproject/galaxy/commit/979bdd44c60d5aab27e472b19afa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix drilldown tests
Commit: 05923e210c41e0f3a6d14a3bd914356c042f4670
https://github.com/galaxyproject/galaxy/commit/05923e210c41e0f3a6d14a3bd914…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Undo name change for workflow regex
Commit: 9863e35368066975fe049adee716c5cabad4c60f
https://github.com/galaxyproject/galaxy/commit/9863e35368066975fe049adee716…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M test/unit/tools/test_data_parameters.py
Log Message:
-----------
Attempt to remove value_mapper parsing
Commit: 29cfd1635879987de9d1efc49d704894454a3ddf
https://github.com/galaxyproject/galaxy/commit/29cfd1635879987de9d1efc49d70…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M test/unit/tools/test_parameter_parsing.py
Log Message:
-----------
Fix test_parameter_parsing
Commit: 474c9a26c495ddddeb6ba7c1966de6ae32cedea7
https://github.com/galaxyproject/galaxy/commit/474c9a26c495ddddeb6ba7c1966d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/webapps/tool_shed/repository/tool_form.mako
M test/unit/tools/test_data_parameters.py
Log Message:
-----------
Fix toolshed tool form preview, import order
Commit: 6b40607e7917b98c481c4e47ac31d31698ce2660
https://github.com/galaxyproject/galaxy/commit/6b40607e7917b98c481c4e47ac31…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove debug output
Commit: 0ef6f7826c621235beef70e8e4c3352d2ab2e2b6
https://github.com/galaxyproject/galaxy/commit/0ef6f7826c621235beef70e8e4c3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Move controller build endpoint to api
Commit: 057485b6f6a8c545478907d01bd6ceadfea0d1f6
https://github.com/galaxyproject/galaxy/commit/057485b6f6a8c545478907d01bd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Import exception, fix parameter names
Commit: a537daa9ed24fe4a4fd7c9e7c54ba30f6de6e156
https://github.com/galaxyproject/galaxy/commit/a537daa9ed24fe4a4fd7c9e7c54b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Move run form model builder to workflow data manager
Commit: b2014fe44ce7b5af42956cf74cd6e75c51a8df0f
https://github.com/galaxyproject/galaxy/commit/b2014fe44ce7b5af42956cf74cd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Disable target history specification for run workflow form
Commit: 2c79755ba2fb752418d7405efdfdcd46bf14d8a4
https://github.com/galaxyproject/galaxy/commit/2c79755ba2fb752418d7405efdfd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Fix stored/workflow handling
Commit: 667d5e83cb6ccb7b46084b73101cb85cc81dd9fa
https://github.com/galaxyproject/galaxy/commit/667d5e83cb6ccb7b46084b73101c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/webapps/tool_shed/repository/tool_form.mako
Log Message:
-----------
Fix value parsing
Commit: 21b5246c913fbf5ae8361f359e17252718f1f87d
https://github.com/galaxyproject/galaxy/commit/21b5246c913fbf5ae8361f359e17…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Remove unused data manager
Commit: c5d00518fe409d4876c18ceaeeef2ad5b6829385
https://github.com/galaxyproject/galaxy/commit/c5d00518fe409d4876c18ceaeeef…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Fix error messages
Commit: 86719ce90e2cb8ee8439b2f4e8a947cc239e1957
https://github.com/galaxyproject/galaxy/commit/86719ce90e2cb8ee8439b2f4e8a9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Remove redundant imports
Commit: 675398c91263eaed37007b76e4856a6d81f888a3
https://github.com/galaxyproject/galaxy/commit/675398c91263eaed37007b76e485…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Use message exception to parse errors
Commit: a0da06d842a6488ee355c0cf37c06f7ffb8ee837
https://github.com/galaxyproject/galaxy/commit/a0da06d842a6488ee355c0cf37c0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Revise comment
Commit: 05b1c988961e9e002e10d4e4cc21f49ff4ab958a
https://github.com/galaxyproject/galaxy/commit/05b1c988961e9e002e10d4e4cc21…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Add basic step version changes notification
Commit: 680e34c1adf87e3f6181bc2d6508f3f5ab84c903
https://github.com/galaxyproject/galaxy/commit/680e34c1adf87e3f6181bc2d6508…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix form preview height style
Commit: 80b5e5da91cdf65b8f06e75a9a6b2c202b94d409
https://github.com/galaxyproject/galaxy/commit/80b5e5da91cdf65b8f06e75a9a6b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-portlet.js
M static/style/blue/base.css
Log Message:
-----------
Remove unused portlet footer
Commit: 1ab673a4ed5de36db49e24edae821d226040d183
https://github.com/galaxyproject/galaxy/commit/1ab673a4ed5de36db49e24edae82…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Fix padding distance
Commit: 9dc412921e5b5446aa4493aca8c7c0105f7d0725
https://github.com/galaxyproject/galaxy/commit/9dc412921e5b5446aa4493aca8c7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix bottom margin
Commit: bb91a10a4cc17f73a051ffec41b796290505b35d
https://github.com/galaxyproject/galaxy/commit/bb91a10a4cc17f73a051ffec41b7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M Makefile
Log Message:
-----------
modify target for tool schema html builder to use pandoc
this is @jmchilton committing as @martenson...pssst
Commit: 7a736818a6c32615c396a2a18d9ebd884ddccebb
https://github.com/galaxyproject/galaxy/commit/7a736818a6c32615c396a2a18d9e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Avoid inheritance in tool-form view
Avoid inheritance for workflow editor form
Fix test cases
Commit: f3c79e6aa97d8d8bf319c4e9105f0b68f09fda54
https://github.com/galaxyproject/galaxy/commit/f3c79e6aa97d8d8bf319c4e9105f…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M templates/webapps/galaxy/dataset/copy_view.mako
Log Message:
-----------
Fix for displaying empty history message in copy datasets. Likely cause is change from a list to a generator at some point.
Commit: 55582a790312a70324fd0dbbb1f6ea00cd992b9c
https://github.com/galaxyproject/galaxy/commit/55582a790312a70324fd0dbbb1f6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
add TS deployments to freeze/release procedures
Commit: 0e324460165900cfba231bc729006f80f46b95e2
https://github.com/galaxyproject/galaxy/commit/0e324460165900cfba231bc72900…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Bump pysam, remove 'already_compressed' usage due to new wheel with autodetect
Commit: 356367fc73185de2bf0dd932ea19d3a4eb4be2c3
https://github.com/galaxyproject/galaxy/commit/356367fc73185de2bf0dd932ea19…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
Fix for copy datasets to respect the '-OR-' and only copy to a new history when name is provided.
Commit: c595ace8da858f9cc7718060cbd29515578932e5
https://github.com/galaxyproject/galaxy/commit/c595ace8da858f9cc7718060cbd2…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M templates/webapps/galaxy/dataset/copy_view.mako
Log Message:
-----------
Add "All" and "None" buttons to copy dataset view.
Commit: fb56a799fd0a0823df82c9946fea70df7764a18d
https://github.com/galaxyproject/galaxy/commit/fb56a799fd0a0823df82c9946fea…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M .gitignore
M Makefile
A doc/parse_gx_xsd.py
A doc/schema_template.md
Log Message:
-----------
Merge pull request #2936 from jmchilton/xsd_docs
XSD Generated Tool Documentation.
Commit: 623110d85fb3d4b8d742fed315c28fb35d3a9595
https://github.com/galaxyproject/galaxy/commit/623110d85fb3d4b8d742fed315c2…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M templates/webapps/galaxy/dataset/copy_view.mako
Log Message:
-----------
Style tweak.
Commit: 51a6d849342f57d426a762ef6fe51e049466e265
https://github.com/galaxyproject/galaxy/commit/51a6d849342f57d426a762ef6fe5…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-22 (Thu, 22 Sep 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #2952 from martenson/adjust-release-check
add TS deployments to freeze/release procedures checklist
Commit: 42ebe00c060d6fcbc69fd16973995c33aba48207
https://github.com/galaxyproject/galaxy/commit/42ebe00c060d6fcbc69fd1697399…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Add listener to properly clean up deferred form building processes
Commit: 2cf7b8ee15856626bff5dfad735023a43ace978b
https://github.com/galaxyproject/galaxy/commit/2cf7b8ee15856626bff5dfad7350…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/utils/utils.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/utils/utils.js
Log Message:
-----------
Fix status handling for ajax requests
Commit: c5a51967173b7e5b0ecf6bbb1340db9ff54a3aed
https://github.com/galaxyproject/galaxy/commit/c5a51967173b7e5b0ecf6bbb1340…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/style/less/base.less
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
M static/style/blue/base.css
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Change wording to be more clear about how workflow output cleanup works. Also adjust styling so that the rows in the workflow editor box are less smashed together.
Commit: 317fb472c96296c6de4d094b7236b9c3f25610da
https://github.com/galaxyproject/galaxy/commit/317fb472c96296c6de4d094b7236…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Commit: 7a604c67d95f51f0afdaa980d01ab4061b4631f0
https://github.com/galaxyproject/galaxy/commit/7a604c67d95f51f0afdaa980d01a…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M scripts/tool_shed/build_ts_whoosh_index.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Commit: 4de55ae51a64c34ab3636e58ea35f43904969d18
https://github.com/galaxyproject/galaxy/commit/4de55ae51a64c34ab3636e58ea35…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Document setting column names in tool XSD.
This is a transplant of a @yhoogstrate wiki update to the XSD docs.
Commit: 277d3c3e58d28904752674c9210f02b88e481eb7
https://github.com/galaxyproject/galaxy/commit/277d3c3e58d28904752674c9210f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
Log Message:
-----------
Slight wording tweak.
Commit: 5549a9ee2bd01940254c49e58ab143d4aa95049a
https://github.com/galaxyproject/galaxy/commit/5549a9ee2bd01940254c49e58ab1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Fix link in galaxy.xsd.
Commit: e8f35310ba581e8f88d719053979c4c3603c930a
https://github.com/galaxyproject/galaxy/commit/e8f35310ba581e8f88d719053979…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M doc/schema_template.md
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Revise and improve ``version_command`` tag.
- Include deprecated ``interpreter`` tag in XSD. (Closes galaxyproject/planemo#574)
- Allow the use of ``$__tool_directory__`` in interpreter command (so we can actually call ``interpreter`` deprecated).
- Include sample tools of both of these styles.
- General improvements to the version command documentation.
Commit: 4df2530847ffee6d280f841c39beabaf7163d5f0
https://github.com/galaxyproject/galaxy/commit/4df2530847ffee6d280f841c39be…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M templates/webapps/galaxy/dataset/copy_view.mako
Log Message:
-----------
Merge pull request #2957 from blankenberg/copy_datasets
Add "All" and "None" buttons to copy dataset view. And fix 2 minor bugs
Commit: e3346e1d273b277445844e38e9e8d29873b4d619
https://github.com/galaxyproject/galaxy/commit/e3346e1d273b277445844e38e9e8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M .gitignore
M Makefile
A doc/parse_gx_xsd.py
A doc/schema_template.md
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
M templates/webapps/galaxy/dataset/copy_view.mako
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge branch 'dev' into strip_run_form_mako
Commit: cbb957028f0c8b740e7b00d1315262dbe55a6b82
https://github.com/galaxyproject/galaxy/commit/cbb957028f0c8b740e7b00d13152…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #2965 from jmchilton/more_action_docs
Document setting column names in tool XSD.
Commit: 5095fc02c4cfb830748179c29ea9e1b1aaf0b455
https://github.com/galaxyproject/galaxy/commit/5095fc02c4cfb830748179c29ea9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-25 (Sun, 25 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M test/unit/workflows/test_run_parameters.py
Log Message:
-----------
Remove internal api endpoint, merge into invocations endpoint
Commit: 7f19ba817c4d8e7d82380bd6fe8d03a7247488f3
https://github.com/galaxyproject/galaxy/commit/7f19ba817c4d8e7d82380bd6fe8d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-25 (Sun, 25 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/qunit/tests/form_tests.js
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge pull request #2935 from guerler/strip_run_form_mako
Strip workflow run mako
Commit: 9d9e5f026dff5523e7e6aef1a9442c872f5fb77c
https://github.com/galaxyproject/galaxy/commit/9d9e5f026dff5523e7e6aef1a944…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M .gitignore
M Makefile
A doc/parse_gx_xsd.py
A doc/schema_template.md
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
M templates/webapps/galaxy/dataset/copy_view.mako
M test/shed_functional/functional/test_1400_review_migration_stages.py
Log Message:
-----------
Merge branch 'dev' into unite_api
Commit: c840730101823107396104dcc7364534577a2dd4
https://github.com/galaxyproject/galaxy/commit/c840730101823107396104dcc736…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Convert dict keys to integers
Commit: 9a9726e9a174a230b3a71bdb40bceb9e5b0d28c7
https://github.com/galaxyproject/galaxy/commit/9a9726e9a174a230b3a71bdb40bc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Fix name generation
Commit: 25ca456697f30671290859fbbcc14b126f2bbd51
https://github.com/galaxyproject/galaxy/commit/25ca456697f30671290859fbbcc1…
Author: yhoogstrate <y.hoogstrate(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
A test/functional/tools/metadata_column_names.xml
Log Message:
-----------
Fuctional test case for testing column names as meta-data
Commit: 838fad39a14674986680edfccfbd24232308c07d
https://github.com/galaxyproject/galaxy/commit/838fad39a14674986680edfccfbd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Add details to error modal
Commit: 1d16200759895b6ede6c38655d085fa7bb0a1e17
https://github.com/galaxyproject/galaxy/commit/1d16200759895b6ede6c38655d08…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Refactor recent toolbox changes for galaxy-lib.
The abstracttoolbox class is supposed to shield Galaxy from the internals of the toolbox organization and vice versa, so having a reload method that uses Galaxy-specific queueing stuff is less than ideal. The concrete toolbox class is where I have been putting such functionality.
In addition to this being the abstract design I prefer, it is definitely needed for galaxy-lib which contains the abstracttoolbox but not the concrete toolbox or the queue worker functionality.
xref #2840
Commit: 780473a751ae52868e29b4e34ba2b0894598dc7b
https://github.com/galaxyproject/galaxy/commit/780473a751ae52868e29b4e34ba2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #2971 from jmchilton/galaxy-lib-import-fix
Refactor recent toolbox changes for galaxy-lib.
Commit: 8414e909a664855a82eda19b9a9fa26cf9178c3f
https://github.com/galaxyproject/galaxy/commit/8414e909a664855a82eda19b9a9f…
Author: yhoogstrate <y.hoogstrate(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Registration of metadata column name test into appropriate XML file - thanks to @nsoranzo
Commit: 750cb7c5843fee4c82f7b028fa59d718a0629927
https://github.com/galaxyproject/galaxy/commit/750cb7c5843fee4c82f7b028fa59…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M doc/schema_template.md
Log Message:
-----------
encourage bug reporting in tool schema
Commit: 051d2b285487fb99a065448b20f69f0d82d3a100
https://github.com/galaxyproject/galaxy/commit/051d2b285487fb99a065448b20f6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M doc/schema_template.md
Log Message:
-----------
Merge pull request #2972 from martenson/tool-schema-report
encourage bug reporting in tool schema document
Commit: 8b452c9dc3dca9c4ba8804e0a3e6edd8d06946c0
https://github.com/galaxyproject/galaxy/commit/8b452c9dc3dca9c4ba8804e0a3e6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Remove invalid attribute metadata_name from param examples in XSD docs.
Pointed out by @peterjc in https://github.com/galaxyproject/tools-iuc/pull/964#issuecomment-249632638.
Commit: 0a767d4d5343d7eaf3697373922d056251c5b802
https://github.com/galaxyproject/galaxy/commit/0a767d4d5343d7eaf3697373922d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix error handling
Commit: 0df6ff9f2d7d841b322ee690a84ec8baa822b336
https://github.com/galaxyproject/galaxy/commit/0df6ff9f2d7d841b322ee690a84e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #2974 from jmchilton/schema_fix_0
Remove invalid attribute metadata_name from param examples in XSD docs.
Commit: 9eba273202873abab5b9f302a9c2ae1cf21c7431
https://github.com/galaxyproject/galaxy/commit/9eba273202873abab5b9f302a9c2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M test/unit/test_galaxy_mapping.py
Log Message:
-----------
Optimized workflow invocation step update.
Commit: 002d974f8adae4cfc52c434c46c4966ac90918bd
https://github.com/galaxyproject/galaxy/commit/002d974f8adae4cfc52c434c46c4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/requirements.py
Log Message:
-----------
Merge pull request #2790 from jmchilton/docker_container_xml
More configurability for containerized jobs
Commit: 7ecf9377bf3780faa2bb93594cf41435a15ff40a
https://github.com/galaxyproject/galaxy/commit/7ecf9377bf3780faa2bb93594cf4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Fix import order in containers.py (broken in cad4002efed5547ccc1f89a3a45d2d4b9b12f76d).
Commit: 8ff8af7b248b79436113e03d3c01e2cc4cd2a88c
https://github.com/galaxyproject/galaxy/commit/8ff8af7b248b79436113e03d3c01…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/tools/deps/containers.py
Log Message:
-----------
Merge pull request #2975 from jmchilton/fix_import_order
Fix import order in containers.py
Commit: 8966b741317431275100c24ab3cc69a221de646c
https://github.com/galaxyproject/galaxy/commit/8966b741317431275100c24ab3cc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
Log Message:
-----------
Swap to section row selector
Commit: 32064b338d619031112298dc489338cdbc67ec5b
https://github.com/galaxyproject/galaxy/commit/32064b338d619031112298dc4893…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/model/mapping.py
Log Message:
-----------
Lazy load workflow invocation steps
Fix job handler going OOM when executing Job.set_final_state()
for a step processing a 30K elements collection in parallel.
Commit: 8054da9fb4d858b7ff9dd461f8baa923fea99425
https://github.com/galaxyproject/galaxy/commit/8054da9fb4d858b7ff9dd461f8ba…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M doc/source/project/issues.rst
Log Message:
-----------
Update issues.rst
Commit: 23fc1e5d577291a86ba9eed1e027ba7516bbfb9d
https://github.com/galaxyproject/galaxy/commit/23fc1e5d577291a86ba9eed1e027…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/model/mapping.py
Log Message:
-----------
Fix import order and Python3 compatibility for lib/galaxy/model/mapping.py
Commit: aa70a97e1e570507121320d9f2370265fd25fca8
https://github.com/galaxyproject/galaxy/commit/aa70a97e1e570507121320d9f237…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M templates/webapps/galaxy/library/common/common.mako
Log Message:
-----------
Merge pull request #2819 from SANBI-SA/upload_admin_line_endings
Functionality to allow admins to switch on/off the line endings conversion on import
Commit: 477d3f9ae94acf2b9c57eba641c2dcdd66d5af27
https://github.com/galaxyproject/galaxy/commit/477d3f9ae94acf2b9c57eba641c2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
A test/api/test_workflow_input_params.ga
M test/api/test_workflows.py
Log Message:
-----------
Add batch mode test case for invocations api
Commit: 10703fac3a00a854bb3d4d548ab1dd22485199c5
https://github.com/galaxyproject/galaxy/commit/10703fac3a00a854bb3d4d548ab1…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-27 (Tue, 27 Sep 2016)
Changed paths:
M doc/source/project/issues.rst
Log Message:
-----------
Merge pull request #2976 from martenson/issues-on-par-with-reality
bring issues.rst on par with reality
Commit: 695a759c9d8301ef447cd30a2c2efd4ef958e79e
https://github.com/galaxyproject/galaxy/commit/695a759c9d8301ef447cd30a2c2e…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/model/mapping.py
Log Message:
-----------
Merge pull request #2978 from nsoranzo/lazy_workflow_invocation
Lazy load workflow invocation steps
Commit: ab68b951da7a766f06cc5fbbfaea34a2ea1b5dac
https://github.com/galaxyproject/galaxy/commit/ab68b951da7a766f06cc5fbbfaea…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M test/base/interactor.py
M test/functional/tools/metadata_column_names.xml
Log Message:
-----------
Implement metadata testing for list metadata.
Commit: efbc06eb0178f495d1581aec7a8c1467af93f2d7
https://github.com/galaxyproject/galaxy/commit/efbc06eb0178f495d1581aec7a8c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/genomes.py
Log Message:
-----------
Cleanup 97532515ea24325ba26877696991b24401733ee6.
Commit: 860c2854b78ac4c6aff2c8524a42225476f8b513
https://github.com/galaxyproject/galaxy/commit/860c2854b78ac4c6aff2c8524a42…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M test/base/interactor.py
A test/functional/tools/metadata_column_names.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #2970 from yhoogstrate/functional_test_metadata_columns
Fuctional test case for testing column names as meta-data
Commit: 98ea43700dd635b6b0c7d6a274d5f3a22ba7829b
https://github.com/galaxyproject/galaxy/commit/98ea43700dd635b6b0c7d6a274d5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
Log Message:
-----------
Update hashes for new pysam wheel.
Commit: fcd86c5e586256438aa8b53035ecf2e1f1e98429
https://github.com/galaxyproject/galaxy/commit/fcd86c5e586256438aa8b53035ec…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Merge pull request #2953 from dannon/pysam_update_gx5
Bump pysam, remove 'already_compressed' usage due to new wheel with a…
Commit: 7d2e3be0b0e989a0ffe72bd8e974998a30353357
https://github.com/galaxyproject/galaxy/commit/7d2e3be0b0e989a0ffe72bd8e974…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Update sqlalchemy to 1.0.15 (from 1.0.8). This is likely the last 1.0 series release before we'll be able to upgrade to a live 1.1.
Commit: 1fee06e4e360f442e2e621e084ca3b313b07138a
https://github.com/galaxyproject/galaxy/commit/1fee06e4e360f442e2e621e084ca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-28 (Wed, 28 Sep 2016)
Changed paths:
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #2979 from dannon/sqlalchemy_1.0.15
Update sqlalchemy to 1.0.15 (from 1.0.8). This is likely the last 1.…
Commit: 991d81cdbeeca43891b2ed5464c73052fbe20ef3
https://github.com/galaxyproject/galaxy/commit/991d81cdbeeca43891b2ed5464c7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix phrasing of error message
Commit: 3d7bfeb6dd08b0241d8fa75f37c5010762146eeb
https://github.com/galaxyproject/galaxy/commit/3d7bfeb6dd08b0241d8fa75f37c5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Revise target url
Commit: 1cb67308771edf40716ef5f30f4321051debc4bb
https://github.com/galaxyproject/galaxy/commit/1cb67308771edf40716ef5f30f43…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Always return a list for formats with batch mode option
Commit: e34019e52806fde224781cfe3bc408b633f86179
https://github.com/galaxyproject/galaxy/commit/e34019e52806fde224781cfe3bc4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Improve invocations success message
Commit: 3545a0ef1f8a2fbde86558fcaf5da43e9563710b
https://github.com/galaxyproject/galaxy/commit/3545a0ef1f8a2fbde86558fcaf5d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Remove unused history wait
Commit: 6f7e9cd5df6eb444974e3d45f1df11f1e3f77281
https://github.com/galaxyproject/galaxy/commit/6f7e9cd5df6eb444974e3d45f1df…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Use hid from hda
Commit: b1eaf85480fbfef5166925294257e2b2cc954b4d
https://github.com/galaxyproject/galaxy/commit/b1eaf85480fbfef5166925294257…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Fix indent
Commit: 1cc8e04c819487c898c09471132b385642dd7b8e
https://github.com/galaxyproject/galaxy/commit/1cc8e04c819487c898c09471132b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form.js.map
Log Message:
-----------
Merge all errors from batch mode run for regular tool executions
Commit: 11b4f3a60c3f24ddbfdf1421391c9b443060a3cf
https://github.com/galaxyproject/galaxy/commit/11b4f3a60c3f24ddbfdf1421391c…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Fix import order and Python3 compatibility for tools/
xref #1715
Commit: 7dadb932d827ee168acefacbf041dad671d36c7f
https://github.com/galaxyproject/galaxy/commit/7dadb932d827ee168acefacbf041…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M test/unit/test_galaxy_mapping.py
Log Message:
-----------
Merge pull request #2973 from jmchilton/optimize_invocation_update
Optimized workflow invocation step update.
Commit: 46d05ba08017cf10467eb0334272e48733c9f684
https://github.com/galaxyproject/galaxy/commit/46d05ba08017cf10467eb0334272…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
A doc/parse_gx_xsd.py
A doc/schema_template.md
M doc/source/project/issues.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/base/interactor.py
A test/functional/tools/metadata_column_names.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/form_tests.js
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/unittest_utils/galaxy_mock.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 494d50f52c33a7465e0d466a3e43fba9fd5a1dbd
https://github.com/galaxyproject/galaxy/commit/494d50f52c33a7465e0d466a3e43…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Repack client
Commit: e14fe506434e55d999995b3da115c7a36f7376be
https://github.com/galaxyproject/galaxy/commit/e14fe506434e55d999995b3da115…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/workflow/run_request.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M test/api/test_workflows.py
Log Message:
-----------
Use order_index instead of step_id
Commit: a1158a79059a47cd928eee2acdbb81df9fbdabcb
https://github.com/galaxyproject/galaxy/commit/a1158a79059a47cd928eee2acdbb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge pull request #2983 from nsoranzo/python3
Fix import order and Python3 compatibility for tools/
Commit: 67eb2c6530bd62f4b6542937f38f373e6022c000
https://github.com/galaxyproject/galaxy/commit/67eb2c6530bd62f4b6542937f38f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/run_request.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M test/api/test_workflows.py
Log Message:
-----------
Use parameters/batch instead of input_params
Commit: 70df25e74b306337e18ce0c2d8291a998da23024
https://github.com/galaxyproject/galaxy/commit/70df25e74b306337e18ce0c2d829…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
A test/api/test_workflow_batch.ga
R test/api/test_workflow_input_params.ga
M test/api/test_workflows.py
Log Message:
-----------
Rename test associated workflow export
Commit: 1a91c603892f7ea574197de67f738df6b7008dd8
https://github.com/galaxyproject/galaxy/commit/1a91c603892f7ea574197de67f73…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Fix startswith method spelling
Introduced in commit 4b2e0c84e19001c8071b374a8e7daf609bb3aa88
Commit: ed7bba5e2027bf239bf86359b68a360149c027dd
https://github.com/galaxyproject/galaxy/commit/ed7bba5e2027bf239bf86359b68a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Increased consistency in backend workflow run code.
Rename build_workflow_run_config to build_workflow_run_configs since it sometimes returned a list, make it always return a list, one path out of run_request.py:build_workflow_run_configs, ensure batch parameter is respected and throw an exception if it is not and build_workflow_run_configs returns multiple invocations.
Commit: c71c1300a2f2797a1009c1c86c9c9449b42e05d5
https://github.com/galaxyproject/galaxy/commit/c71c1300a2f2797a1009c1c86c9c…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/datatypes/data.py
Log Message:
-----------
Merge pull request #2990 from nsoranzo/fix_for_2761
Fix startswith method spelling
Commit: 8166276679cb1d1bf90d9cf473102b3e2eda3b99
https://github.com/galaxyproject/galaxy/commit/8166276679cb1d1bf90d9cf47310…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Do not copy tags from source history
Commit: 8fab4f141b93e298487e1a5ed58fda24289be7ef
https://github.com/galaxyproject/galaxy/commit/8fab4f141b93e298487e1a5ed58f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Unify workflow API history options across approaches.
The old variant of specifying a history attribute should work with new batch parameter mode and the new variant of specifing new_history_name or history_id should work with the existing invocation API stuff.
Commit: f4ca27d50dbac3d89ad758262633777545ee32f4
https://github.com/galaxyproject/galaxy/commit/f4ca27d50dbac3d89ad758262633…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Add error response to validate expansion result
Commit: 5b70453e5ea2d98052635c509ee5502574144c06
https://github.com/galaxyproject/galaxy/commit/5b70453e5ea2d98052635c509ee5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Log Message:
-----------
Merge remote-tracking branch 'guerler/unite_api' into unite_api_history
Conflicts:
lib/galaxy/workflow/run_request.py
Commit: 2eadece71e8ff8cff76ed58d56cb5eba7ac99c87
https://github.com/galaxyproject/galaxy/commit/2eadece71e8ff8cff76ed58d56cb…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Add flake8 pinning to Branch procedures
Commit: ab2a5198afeb0b651643b84c0dd3eb6a0e611bb6
https://github.com/galaxyproject/galaxy/commit/ab2a5198afeb0b651643b84c0dd3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Resolve this comment/discussion (https://github.com/galaxyproject/galaxy/pull/2969#issuecomment-250830186).
Commit: 92034e67766c0e608b8cec6c63e29e3405e80333
https://github.com/galaxyproject/galaxy/commit/92034e67766c0e608b8cec6c63e2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Revert to an exception instead of an assertion.
I'm close to winning @guerler over - but not quite there yet.
Commit: 72980bc967a8fb7b988b4c33a79af9c3af94bcc2
https://github.com/galaxyproject/galaxy/commit/72980bc967a8fb7b988b4c33a79a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Log Message:
-----------
Merge remote-tracking branch 'guerler/unite_api' into unite_api_history
Conflicts:
lib/galaxy/workflow/run_request.py
Commit: 3d4e02f1314cdeeae6fc6285e7b0c35fb2b6f136
https://github.com/galaxyproject/galaxy/commit/3d4e02f1314cdeeae6fc6285e7b0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Fixup previous commits bugs.
Commit: 4fea03acc917089498cb2a897e931a5d1cec8a7b
https://github.com/galaxyproject/galaxy/commit/4fea03acc917089498cb2a897e93…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Use explicit order_index when assigning workflow steps
Commit: 55cce84189510e14b55a042168e5f63c71be7fe3
https://github.com/galaxyproject/galaxy/commit/55cce84189510e14b55a042168e5…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Reload metadata and lib tools on toolbox reload
Should close #2988.
Commit: c67e4ac1a391348fdac942ebe2918cb7e0e08235
https://github.com/galaxyproject/galaxy/commit/c67e4ac1a391348fdac942ebe291…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Test case
Commit: 66a5bd45bd3c72e497b2098337de652b2c5d5f51
https://github.com/galaxyproject/galaxy/commit/66a5bd45bd3c72e497b2098337de…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #2991 from nsoranzo/fix_for_2665
Add flake8 pinning to Branch procedures
Commit: 9df99d2bb0f5c34c66f1d0730c012b5cd268899b
https://github.com/galaxyproject/galaxy/commit/9df99d2bb0f5c34c66f1d0730c01…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M test/api/test_workflows.py
Log Message:
-----------
Merge remote-tracking branch 'guerler/unite_api' into unite_api_history
Commit: 0263c3259ebcf7d604bfc9da8ba1bb69800a27aa
https://github.com/galaxyproject/galaxy/commit/0263c3259ebcf7d604bfc9da8ba1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Refactor run_request to reuse step parameter normalization.
Lessens the difference between GUI and API approaches.
Commit: eb288cd4e122b0c5ff11a75fbac34374b080bc3a
https://github.com/galaxyproject/galaxy/commit/eb288cd4e122b0c5ff11a75fbac3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Refactor build_workflow_run_configs toward unification of API and UI approaches.
Commit: a2e265e8b148da7e4a6ba50eb9b64cdaf6765a93
https://github.com/galaxyproject/galaxy/commit/a2e265e8b148da7e4a6ba50eb9b6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Refactor build_workflow_run_configs toward unification of API and UI approaches.
Swap expansion of raw parameters and normalization of parmeters so that we can move the loop outside of the conditional ... and thus elimiante the conditional that distinguishes between API and UI approaches.
Commit: e60fd0490526e76f58210151d9ea6090d9277317
https://github.com/galaxyproject/galaxy/commit/e60fd0490526e76f58210151d9ea…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Refine workflow target history handling with bug fix and improved error message.
Commit: b106c48b68f87b2c9008e6f03b5cdb51b951051a
https://github.com/galaxyproject/galaxy/commit/b106c48b68f87b2c9008e6f03b5c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/workflow/run_request.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M test/api/test_workflows.py
Log Message:
-----------
Unify build_workflow_run_configs for API and UI approaches to running workflows.
No more branches - the method runs top to bottom for each approach. One loop for batching regardless and completely available to all API options. Only call WorkflowRunConfig in one place. Remove duplicate fetching of replacement_params. One call to _normalize_step_parameters.
Commit: aaf5cc4075fcf3951850b979b4b4eec288fd5393
https://github.com/galaxyproject/galaxy/commit/aaf5cc4075fcf3951850b979b4b4…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/workflow/run_request.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #13 from jmchilton/unite_api_history
Unify workflow API history options across approaches.
Commit: dc209c7a003bbc63d590cbbc45fbdf48340bbe8c
https://github.com/galaxyproject/galaxy/commit/dc209c7a003bbc63d590cbbc45fb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Encode unencoded step id when exposing workflow dictionary for execution
Commit: 76201eba45c39e9b5b62be865bc56331bb775d57
https://github.com/galaxyproject/galaxy/commit/76201eba45c39e9b5b62be865bc5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-30 (Fri, 30 Sep 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Move get target history out of build_workflow_run_configs
Commit: 5e6af483d799137c2a956d98aad79ee30f636101
https://github.com/galaxyproject/galaxy/commit/5e6af483d799137c2a956d98aad7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-01 (Sat, 01 Oct 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Refactor target history mode validation, remove spaces
Commit: 824f556ea7d04b5141307ede3258850fcc17ed77
https://github.com/galaxyproject/galaxy/commit/824f556ea7d04b5141307ede3258…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/queue_worker.py
Log Message:
-----------
Merge pull request #2992 from mvdbeek/reload_special_tools
Reload metadata and lib tools on toolbox reload
Commit: 0f6ad3f41469816cbb31b6c5a2a663cf30f0ecf1
https://github.com/galaxyproject/galaxy/commit/0f6ad3f41469816cbb31b6c5a2a6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Use order index to link connected datasets
Commit: ce7cf6cc230827c1ad485579a7efd4a2fa807381
https://github.com/galaxyproject/galaxy/commit/ce7cf6cc230827c1ad485579a7ef…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Rename step_id to step_index to avoid confusion
Commit: d5c54907dad35d5ba8578f4d563c36c8b06fa43d
https://github.com/galaxyproject/galaxy/commit/d5c54907dad35d5ba8578f4d563c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/workflow/modules.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Rename step_id to step_index to avoid confusion, fix error message response handling
Commit: 0b03a800abdab4540152adea44ed820cbc2782e0
https://github.com/galaxyproject/galaxy/commit/0b03a800abdab4540152adea44ed…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Improve error display robustness for run workflow form
Commit: f3ce9a927caf193ee7f681553c6209dfa3fd05ff
https://github.com/galaxyproject/galaxy/commit/f3ce9a927caf193ee7f681553c62…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Remove sorting from workflow expansion test cases
Commit: b865952bab1a659e70e65aaf63740d776fbb3249
https://github.com/galaxyproject/galaxy/commit/b865952bab1a659e70e65aaf6374…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
-----------
Add reference to Go-Docker repository and a little blurb.
Commit: 4664a64c15d9989a5fd0589e0551d7a681db8f9e
https://github.com/galaxyproject/galaxy/commit/4664a64c15d9989a5fd0589e0551…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/jobs/runners/godocker.py
Log Message:
-----------
Remove ssl warning disable -- these are good to have/see when using unverified SSL connections.
Commit: ea1879d4410eda95506e9645adada1bc8a2247dc
https://github.com/galaxyproject/galaxy/commit/ea1879d4410eda95506e9645adad…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Remove sorting from last expansion test case
Commit: 00f471156574cb1a5bba3cf62ee26c8dc4a6e41e
https://github.com/galaxyproject/galaxy/commit/00f471156574cb1a5bba3cf62ee2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
Log Message:
-----------
Fix order in workflow expansion
Commit: c2f1b635cc65aafd32309b788d809c5d6cf53615
https://github.com/galaxyproject/galaxy/commit/c2f1b635cc65aafd32309b788d80…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-03 (Mon, 03 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/meta.py
M test/api/test_workflows.py
Log Message:
-----------
Rely on deterministic invocations order in batch mode test case
Commit: 4d871fa734e0982e685fb1bf356f4147ff1ae143
https://github.com/galaxyproject/galaxy/commit/4d871fa734e0982e685fb1bf356f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M test/api/test_workflows.py
Log Message:
-----------
Check both invocation orders when using the new batch mode feature
Commit: b46d55e30fd3f8a2832130dd3f917082f442836f
https://github.com/galaxyproject/galaxy/commit/b46d55e30fd3f8a2832130dd3f91…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/webhooks.js
A config/plugins/webhooks/history_test1/config/history_test1.yml
A config/plugins/webhooks/history_test2/config/history_test2.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
add new entry point for History Panel menu
Commit: 17c4af285d75e4a271880b37f4727df59987655a
https://github.com/galaxyproject/galaxy/commit/17c4af285d75e4a271880b37f472…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
Log Message:
-----------
Docstring fixes for galaxy.exceptions and galaxy.jobs.metrics.
xref https://github.com/galaxyproject/galaxy-lib/pull/21.
Rebase with spelling fixes thanks to @nsoranzo.
Commit: d9af95b401ebec1db5cd6653f5ebbb9a7fd5c3f5
https://github.com/galaxyproject/galaxy/commit/d9af95b401ebec1db5cd6653f5eb…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
Log Message:
-----------
Merge pull request #3003 from jmchilton/docstrings1
Docstring fixes for galaxy.exceptions and galaxy.jobs.metrics.
Commit: 329ee052510c0c720ae5d44bac23becf639f6506
https://github.com/galaxyproject/galaxy/commit/329ee052510c0c720ae5d44bac23…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Hide children elements instead of destroying them upon successful workflow submission
Commit: 56721e7a0fe67e9aba55d4b52d97601b75b2beb9
https://github.com/galaxyproject/galaxy/commit/56721e7a0fe67e9aba55d4b52d97…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .travis.yml
M lib/galaxy/util/__init__.py
M setup.cfg
M tox.ini
Log Message:
-----------
Initial docstring linting.
- Apply one docstring lint to the global lint list (D302 - unicode docstrings should start with u""").
- Create an inclusion list with many more docstring checks (public modules need a docstring, white space and quoting issue, check imperative mood and capitializaton). Add a couple modules to this inclusion list.
- Add tox and Travis targets for this linting.
This gives a person who wants to work on improving Galaxy's in-code docstring documentation three ways to "raise the bar" for the project. One could:
- Add more modules to the inclusion list (.ci/flake8_docstrings_include_list.txt). Many more modules should contain docstrings - especially things in galaxy-lib and web controllers.
- Add more checks to the existing inclusion list checks - I'd say D101 and/or D103 first or any of the missing D2XX or D4XX options. D102 seems a bit too ambitious and I worry it'd be too much of a burden.
- Pick some DXXX check that is ignored globally and fix it for the whole project and then remove it from the exclude list in setup.cfg.
Commit: 922d9ee53a9d9400cda622c12d6f79fc190673f6
https://github.com/galaxyproject/galaxy/commit/922d9ee53a9d9400cda622c12d6f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Fix for unite_api branch for API key specification without explicit history target.
It is good to not depend on trans.history being set I think and this is required to fix bioblend tests.
Commit: 5a5d770455f5a41f0630cf6b7fad40a2e0e939e0
https://github.com/galaxyproject/galaxy/commit/5a5d770455f5a41f0630cf6b7fad…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Merge pull request #14 from jmchilton/unite_api_apikey_fix
Fix for unite_api branch for API key specification without explicit history target.
Commit: b595cd3f4775c1435a28ee80159fe16a2b4581b6
https://github.com/galaxyproject/galaxy/commit/b595cd3f4775c1435a28ee80159f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M lib/galaxy/managers/workflows.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/scripts/mvc/tool/tool-form-composite.js
Log Message:
-----------
Always submit either history_id or new history name through run form
Commit: 2ca1af225f8fe1715ef058fd0f516a48d32fa325
https://github.com/galaxyproject/galaxy/commit/2ca1af225f8fe1715ef058fd0f51…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M lib/galaxy/workflow/run_request.py
Log Message:
-----------
Remove trans.history from target history identification
Commit: 240781811e3f6f6b05dc53bee69850745f71d5c2
https://github.com/galaxyproject/galaxy/commit/240781811e3f6f6b05dc53bee698…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove unnecessary line from test cases
Commit: 5595bf2e40687f6e67e34748867f57eedbd7ceab
https://github.com/galaxyproject/galaxy/commit/5595bf2e40687f6e67e34748867f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #3005 from guerler/simplify_basic_py
Remove unnecessary line from parameter unit test cases
Commit: f0f26e0654b2f9f3bdd3a159ea2800745980abd2
https://github.com/galaxyproject/galaxy/commit/f0f26e0654b2f9f3bdd3a159ea28…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
A test/api/test_workflow_batch.ga
M test/api/test_workflows.py
M test/unit/workflows/test_run_parameters.py
Log Message:
-----------
Merge pull request #2969 from guerler/unite_api
Unite workflow execution api endpoints
Commit: 16c2227b93151c31caefa369e17e36cdfb75e381
https://github.com/galaxyproject/galaxy/commit/16c2227b93151c31caefa369e17e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/genomes.py
Log Message:
-----------
Merge pull request #2939 from jj-umn/patch-4
API access to genome fasta index and sequence
Commit: 9ae35cb64a57a67976459de1a9c589f3b70ab3f1
https://github.com/galaxyproject/galaxy/commit/9ae35cb64a57a67976459de1a9c5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M tox.ini
Log Message:
-----------
Fix typo spotted by @nsoranzo.
Commit: b98e49f2bc88e62b4835aa8d23f8d3386f81f66a
https://github.com/galaxyproject/galaxy/commit/b98e49f2bc88e62b4835aa8d23f8…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/history_test1/config/history_test1.yml
M config/plugins/webhooks/history_test2/config/history_test2.yml
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webhooks/__init__.py
M static/maps/layout/menu.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
bug fixes and improvements
Commit: 58e0d6e1a61b06c444b2086d7725e1100d49441a
https://github.com/galaxyproject/galaxy/commit/58e0d6e1a61b06c444b2086d7725…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
A config/plugins/plugin1.xml
A config/plugins/plugin2.xml
A config/plugins/webhooks/plugin1/config/plugin1.yaml
A config/plugins/webhooks/plugin2/config/plugin2.yml
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/webapps/galaxy/api/webhooks.py
A lib/galaxy/webhooks/__init__.py
Log Message:
-----------
add Webhooks draft
Commit: cbbcf3d625a1625e89bbe7c59997d3658d23ea55
https://github.com/galaxyproject/galaxy/commit/cbbcf3d625a1625e89bbe7c59997…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
R config/plugins/plugin1.xml
R config/plugins/plugin2.xml
Log Message:
-----------
remove extra files
Commit: cf1fde577e9b918bacfe2d78d9f2b632a81ee20b
https://github.com/galaxyproject/galaxy/commit/cf1fde577e9b918bacfe2d78d9f2…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/tool/tool-webhooks.js
A client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/plugin2/config/plugin2.yml
A config/plugins/webhooks/plugin2/static/style.css
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
A static/maps/mvc/tool/tool-webhooks.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
A static/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
add very basic plugin system (for tools)
Commit: ac5a0f5a6adea3493549d69627d1d2223b97c09e
https://github.com/galaxyproject/galaxy/commit/ac5a0f5a6adea3493549d69627d1…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin2/config/plugin2.yml
R config/plugins/webhooks/plugin2/static/style.css
A config/plugins/webhooks/xkcd/config/xkcd.yml
A config/plugins/webhooks/xkcd/static/script.js
A config/plugins/webhooks/xkcd/static/styles.css
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/tool/tool-webhooks.js.map
M static/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
add first webhook
Commit: fecf493ecde3590e9da4629a063d5885dde99502
https://github.com/galaxyproject/galaxy/commit/fecf493ecde3590e9da4629a063d…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
A config/plugins/webhooks/phdcomics/config/phdcomics.yaml
A config/plugins/webhooks/phdcomics/helper/__init__.py
A config/plugins/webhooks/phdcomics/static/script.js
A config/plugins/webhooks/phdcomics/static/styles.css
R config/plugins/webhooks/plugin1/config/plugin1.yaml
M config/plugins/webhooks/xkcd/static/script.js
M config/plugins/webhooks/xkcd/static/styles.css
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/tool/tool-webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
add one more plugin
Commit: 239731d45aa5019eecc4d65a771102bb38a79851
https://github.com/galaxyproject/galaxy/commit/239731d45aa5019eecc4d65a7711…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
R client/galaxy/scripts/mvc/tool/tool-webhooks.js
A config/plugins/webhooks/topbar_test/config/topbar_test.yml
M lib/galaxy/webhooks/__init__.py
A static/maps/mvc/webhooks.js.map
A static/scripts/mvc/webhooks.js
Log Message:
-----------
topbar webhooks testing
Commit: d35d99727b76ab71173ad7cccca1a4d66aa9ce70
https://github.com/galaxyproject/galaxy/commit/d35d99727b76ab71173ad7cccca1…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
A config/plugins/plugin1.xml
A config/plugins/plugin2.xml
A config/plugins/webhooks/plugin1/config/plugin1.yaml
A config/plugins/webhooks/plugin2/config/plugin2.yml
Log Message:
-----------
add Webhooks draft
Commit: 1f7a4135318f0d6940e2a65a2b9f7ab29cdb0a41
https://github.com/galaxyproject/galaxy/commit/1f7a4135318f0d6940e2a65a2b9f…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
R config/plugins/plugin1.xml
R config/plugins/plugin2.xml
Log Message:
-----------
remove extra files
Commit: adc92fd31740ebe4fe66bfec32fe14ef5b736c72
https://github.com/galaxyproject/galaxy/commit/adc92fd31740ebe4fe66bfec32fe…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/tool/tool-webhooks.js
M config/plugins/webhooks/plugin2/config/plugin2.yml
A config/plugins/webhooks/plugin2/static/style.css
Log Message:
-----------
add very basic plugin system (for tools)
Commit: d490415b0500dcbadca9a1f959cf0b996abe326e
https://github.com/galaxyproject/galaxy/commit/d490415b0500dcbadca9a1f959cf…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin2/config/plugin2.yml
R config/plugins/webhooks/plugin2/static/style.css
Log Message:
-----------
add first webhook
Commit: 86af65a7d6889086e1f16ef3ef4fcfa77ba3c88e
https://github.com/galaxyproject/galaxy/commit/86af65a7d6889086e1f16ef3ef4f…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin1/config/plugin1.yaml
Log Message:
-----------
add one more plugin
Commit: 4635ff4575ea1a47fac8da2bbb50092cc3352c3f
https://github.com/galaxyproject/galaxy/commit/4635ff4575ea1a47fac8da2bbb50…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
topbar webhooks testing
Commit: 482e0b2bffe992c329f22e4f9b50a34cfd835518
https://github.com/galaxyproject/galaxy/commit/482e0b2bffe992c329f22e4f9b50…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
A config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
R config/plugins/webhooks/topbar_test/config/topbar_test.yml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
renamings and fixes
Commit: 6e534213e12820f69bb849b74aa8924787d9023e
https://github.com/galaxyproject/galaxy/commit/6e534213e12820f69bb849b74aa8…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/masthead_test/static/script.js
M config/plugins/webhooks/phdcomics/helper/__init__.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
- unify webhooks entry point
- simlify webhooks code (on load)
- improve code readability
- clean up
Commit: fce44d257b9d05e68ca4323036e7e509d329e789
https://github.com/galaxyproject/galaxy/commit/fce44d257b9d05e68ca4323036e7…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
M templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
- add new entry point (Workflow)
- temporarily hide masthead webhook (due to instability)
Commit: 3c3819900fd293de1532a4c0a15685927a8fd2dd
https://github.com/galaxyproject/galaxy/commit/3c3819900fd293de1532a4c0a156…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
A config/plugins/webhooks/history_test1/config/history_test1.yml
A config/plugins/webhooks/history_test2/config/history_test2.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
add new entry point for History Panel menu
Commit: 6f109176d16a162b9f5a132927eef13e096bdce4
https://github.com/galaxyproject/galaxy/commit/6f109176d16a162b9f5a132927ee…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M config/plugins/webhooks/history_test1/config/history_test1.yml
M config/plugins/webhooks/history_test2/config/history_test2.yml
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
bug fixes and improvements
Commit: 31674ef5b789b9c9557bb78efaa5d13961744c1d
https://github.com/galaxyproject/galaxy/commit/31674ef5b789b9c9557bb78efaa5…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system
# Conflicts:
# client/galaxy/scripts/layout/menu.js
# client/galaxy/scripts/mvc/tool/tool-form.js
# static/maps/layout/menu.js.map
# static/maps/mvc/tool/tool-form.js.map
# static/scripts/bundled/analysis.bundled.js
# static/scripts/bundled/analysis.bundled.js.map
# static/scripts/bundled/libs.bundled.js
# static/scripts/bundled/libs.bundled.js.map
# static/scripts/layout/menu.js
# static/scripts/mvc/tool/tool-form.js
Commit: be3c347a37fd0a84ff08fbac00af7816158db634
https://github.com/galaxyproject/galaxy/commit/be3c347a37fd0a84ff08fbac00af…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add rgb option for color picker
Commit: c6fca34428bdf62d74ff476f5a1bd4b2b9f97790
https://github.com/galaxyproject/galaxy/commit/c6fca34428bdf62d74ff476f5a1b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove unused value map argument from basic parameter handling
Commit: 2bf0549a371a1a3f683d375233b9b3f5b1e37944
https://github.com/galaxyproject/galaxy/commit/2bf0549a371a1a3f683d375233b9…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M config/plugins/webhooks/xkcd/config/xkcd.yml
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
fix bugs after previous commit
Commit: a2ee8d10af84332bf1afa1e32f0acf9cdb754f0a
https://github.com/galaxyproject/galaxy/commit/a2ee8d10af84332bf1afa1e32f0a…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-modal.js
M doc/source/admin/conda_faq.rst
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-modal.js
Log Message:
-----------
Merge branch 'release_16.07' into dev
Conflicts:
doc/source/admin/conda_faq.rst
static/maps/mvc/ui/ui-modal.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
static/scripts/mvc/ui/ui-modal.js
Commit: f283a6248cc6638c58074286f7dfa3e34a2e1a00
https://github.com/galaxyproject/galaxy/commit/f283a6248cc6638c58074286f7df…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add space
Commit: f6d395c7cb9c217a2c653781a5702a1ae8449342
https://github.com/galaxyproject/galaxy/commit/f6d395c7cb9c217a2c653781a570…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix whitespace after comma
Commit: e93c9b42d648537fed89569373d83f20ebeaf3c7
https://github.com/galaxyproject/galaxy/commit/e93c9b42d648537fed89569373d8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove two unused private functions for data tool parameters
Commit: 5f9bfd5fc078043bce9fa10c0063a1989887aae2
https://github.com/galaxyproject/galaxy/commit/5f9bfd5fc078043bce9fa10c0063…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Add an XSD entry for this new feature.
Commit: a6da9ab00006fc21ebbf511f1210a9685ce9ddfa
https://github.com/galaxyproject/galaxy/commit/a6da9ab00006fc21ebbf511f1210…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
Log Message:
-----------
Rename private function to indicate public use
Commit: 2b9034d597941ad055975fb776506b8de2382c67
https://github.com/galaxyproject/galaxy/commit/2b9034d597941ad055975fb77650…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M doc/source/api/guidelines.rst
Log Message:
-----------
Update some old information in API guideline docs.
Commit: c03748dd49c060a68d07bce56eae33e0ba154414
https://github.com/galaxyproject/galaxy/commit/c03748dd49c060a68d07bce56eae…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-05 (Wed, 05 Oct 2016)
Changed paths:
M doc/source/api/guidelines.rst
Log Message:
-----------
Merge pull request #3011 from jmchilton/api_docs
Update some old information in API guideline docs.
Commit: f599a7b8c025a60781216450f00a81c5a497bfd7
https://github.com/galaxyproject/galaxy/commit/f599a7b8c025a60781216450f00a…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-06 (Thu, 06 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #15 from guerler/XSD_addition
Add an XSD entry for this new feature.
Commit: 59a6d07b7b02f2b23719acdc83122eae89e49b78
https://github.com/galaxyproject/galaxy/commit/59a6d07b7b02f2b23719acdc8312…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-06 (Thu, 06 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-modal.js
M doc/source/admin/conda_faq.rst
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-modal.js
Log Message:
-----------
Merge pull request #3010 from nsoranzo/merge_release_16.07
Merge release_16.07 into dev
Commit: 51aa341fe5ac7859233081af3ce5fab934349b1c
https://github.com/galaxyproject/galaxy/commit/51aa341fe5ac7859233081af3ce5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-06 (Thu, 06 Oct 2016)
Changed paths:
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .travis.yml
M lib/galaxy/util/__init__.py
M setup.cfg
M tox.ini
Log Message:
-----------
Merge pull request #3004 from jmchilton/docstring_lint
Initial docstring linting.
Commit: 5e15d3b79d0fee4f469e2e3a1b0e2acdddeda15c
https://github.com/galaxyproject/galaxy/commit/5e15d3b79d0fee4f469e2e3a1b0e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Use requests in driver_util for better proxy handling
Commit: d0b9e2ca9f19453a74a478426c3e2d2236bf8788
https://github.com/galaxyproject/galaxy/commit/d0b9e2ca9f19453a74a478426c3e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
Log Message:
-----------
Merge pull request #3007 from guerler/remove_unused_value_map
Remove unused value map argument from basic parameter handling
Commit: 2b10e2047293ee95ea8084657c55a5e354ce3b23
https://github.com/galaxyproject/galaxy/commit/2b10e2047293ee95ea8084657c55…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3006 from guerler/add_rgb_option
Add rgb option for color picker
Commit: 5e8da4ec82848407a4f1127da57eed5006b6ea39
https://github.com/galaxyproject/galaxy/commit/5e8da4ec82848407a4f1127da57e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix bare exception.
https://docs.python.org/2/howto/doanddont.html#except
Commit: 9e299e93468041e984518d0992ad4b2041b681f6
https://github.com/galaxyproject/galaxy/commit/9e299e93468041e984518d0992ad…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #3013 from mvdbeek/proxy_planemo
Use requests in driver_util for better proxy handling
Commit: e310453fd0bde9c0c565c6f68b2fcd09942ac49a
https://github.com/galaxyproject/galaxy/commit/e310453fd0bde9c0c565c6f68b2f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/color_param.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Improved docs and testing for color params.
Commit: f72b46198ef7f03533b7d400195828d0976027c4
https://github.com/galaxyproject/galaxy/commit/f72b46198ef7f03533b7d4001958…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
A lib/galaxy/jobs/runners/godocker.py
Log Message:
-----------
Merge pull request #2791 from dannon/godocker
Godocker job runner
Commit: 3345dd4a92b9224a6a4e864326b60c8e92f29ad0
https://github.com/galaxyproject/galaxy/commit/3345dd4a92b9224a6a4e864326b6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #2865 from martenson/forced-wittiness
encourage wittiness in release notes
Commit: a08b849f6db5041dc56173051bc45aaa8c469ae4
https://github.com/galaxyproject/galaxy/commit/a08b849f6db5041dc56173051bc4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/color_param.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3016 from jmchilton/color_followup
Improved docs and testing for color params.
Commit: 604dfb27ce0acba176c059f08642aae7a390ddf0
https://github.com/galaxyproject/galaxy/commit/604dfb27ce0acba176c059f08642…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Fix for reruning tool with workflow resume that is part of a collection.
The special casing of "__identifier__" that occurs here and elsewhere in the code is less than ideal.
Commit: c39f8c92ea47c73e2cef8295e4816f06a6e72f44
https://github.com/galaxyproject/galaxy/commit/c39f8c92ea47c73e2cef8295e481…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Fix for XSD
Commit: 056a7e0d1e7a6e3bb78f22903df6b941b44fad69
https://github.com/galaxyproject/galaxy/commit/056a7e0d1e7a6e3bb78f22903df6…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3020 from bgruening/xsd_fix
Fix for XSD
Commit: 415c7fa67be28885fa92246fb63efdf5bfd777bf
https://github.com/galaxyproject/galaxy/commit/415c7fa67be28885fa92246fb63e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Verify tools coming from cache have correct id.
Commit: 56dfaf003f3239d2475715b478e319ff359e08d4
https://github.com/galaxyproject/galaxy/commit/56dfaf003f3239d2475715b478e3…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix tool reload in 415c7fa67be28885fa92246fb63efdf5bfd777bf
Previous commit changed the if/elif/else logic. The else was now
applying also to cached tools, which it should not. Instead, explicitly
check that we still don't have a tool object.
Commit: 5a72449246be6f0f2fe3955bebf6f42ae89966bc
https://github.com/galaxyproject/galaxy/commit/5a72449246be6f0f2fe3955bebf6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Implement beta support for dynamically discovering mulled containers for dependencies.
Contains all mulled fixes and enhancements through 16.10.7 including several bug fixes from @bgruening.
Commit: e389e1939160dfef7c364785a17869f5de30198b
https://github.com/galaxyproject/galaxy/commit/e389e1939160dfef7c364785a178…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Implement option to require containerization of jobs.
This is great for security in production. For my own greedy concerns, I'm adding it for development however. I don't want someone to be testing mulled containers and accidently run the job locally.
Commit: fdc81bd84a76082249474782367b7b7a59706af3
https://github.com/galaxyproject/galaxy/commit/fdc81bd84a76082249474782367b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository revision
Commit: 2316075f0caf7771bafabbfa00bfe2c5ecdfacec
https://github.com/galaxyproject/galaxy/commit/2316075f0caf7771bafabbfa00bf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M config/job_conf.xml.sample_advanced
M doc/source/admin/conda_faq.rst
M doc/source/api/guidelines.rst
M lib/galaxy/datatypes/data.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M scripts/bootstrap_history.py
M setup.cfg
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-modal.js
A test/api/test_workflow_batch.ga
M test/api/test_workflows.py
M test/base/driver_util.py
A test/functional/tools/color_param.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: b7a25fc653fa30a78d97b2aa23e9a5ad43814694
https://github.com/galaxyproject/galaxy/commit/b7a25fc653fa30a78d97b2aa23e9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Update repository revision to new drawrnajs logo
Commit: 654b5e9322f5c54332c8d8861bc8ed34c6e71a8e
https://github.com/galaxyproject/galaxy/commit/654b5e9322f5c54332c8d8861bc8…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A doc/source/admin/mulled_containers.rst
Log Message:
-----------
Add initial documentation about the new mulled features.
Commit: d821c2745c014bc0e2e2cc31eac8d70bb576ea7e
https://github.com/galaxyproject/galaxy/commit/d821c2745c014bc0e2e2cc31eac8…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
R config/plugins/webhooks/masthead_test/static/script.js
M config/plugins/webhooks/phdcomics/helper/__init__.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
pass trans object into the helper function
Commit: 1a80a0df7f371347976f0b9fb3ff1cb651d4170b
https://github.com/galaxyproject/galaxy/commit/1a80a0df7f371347976f0b9fb3ff…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A doc/source/admin/webhooks.rst
Log Message:
-----------
Add initial docs
Commit: 5361d7c03d23ed4fe4701b2e126f56114673cf7f
https://github.com/galaxyproject/galaxy/commit/5361d7c03d23ed4fe4701b2e126f…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
A config/plugins/plugin1.xml
A config/plugins/plugin2.xml
A config/plugins/webhooks/plugin1/config/plugin1.yaml
A config/plugins/webhooks/plugin2/config/plugin2.yml
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/webapps/galaxy/api/webhooks.py
A lib/galaxy/webhooks/__init__.py
Log Message:
-----------
add Webhooks draft
Commit: a34a1201fc72abff092ccb8c0366b07dfde31987
https://github.com/galaxyproject/galaxy/commit/a34a1201fc72abff092ccb8c0366…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R config/plugins/plugin1.xml
R config/plugins/plugin2.xml
Log Message:
-----------
remove extra files
Commit: 6e66fbeca8741748aa823e34432bd62527096491
https://github.com/galaxyproject/galaxy/commit/6e66fbeca8741748aa823e34432b…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
A client/galaxy/scripts/mvc/tool/tool-webhooks.js
M config/plugins/webhooks/plugin2/config/plugin2.yml
A config/plugins/webhooks/plugin2/static/style.css
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
A static/maps/mvc/tool/tool-webhooks.js.map
A static/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
add very basic plugin system (for tools)
Commit: eb46e70206ba43a5e191153df74aa47dc441ed19
https://github.com/galaxyproject/galaxy/commit/eb46e70206ba43a5e191153df74a…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin2/config/plugin2.yml
R config/plugins/webhooks/plugin2/static/style.css
A config/plugins/webhooks/xkcd/config/xkcd.yml
A config/plugins/webhooks/xkcd/static/script.js
A config/plugins/webhooks/xkcd/static/styles.css
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/tool/tool-webhooks.js.map
M static/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
add first webhook
Commit: 40bcaaecf531920275d8f9f82d5e57bac60c43ae
https://github.com/galaxyproject/galaxy/commit/40bcaaecf531920275d8f9f82d5e…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
A config/plugins/webhooks/phdcomics/config/phdcomics.yaml
A config/plugins/webhooks/phdcomics/helper/__init__.py
A config/plugins/webhooks/phdcomics/static/script.js
A config/plugins/webhooks/phdcomics/static/styles.css
R config/plugins/webhooks/plugin1/config/plugin1.yaml
M config/plugins/webhooks/xkcd/static/script.js
M config/plugins/webhooks/xkcd/static/styles.css
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/tool/tool-webhooks.js.map
M static/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
add one more plugin
Commit: bf4a1aa1a87050e030ead0e5ff8922bcb7338d98
https://github.com/galaxyproject/galaxy/commit/bf4a1aa1a87050e030ead0e5ff89…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
R client/galaxy/scripts/mvc/tool/tool-webhooks.js
A client/galaxy/scripts/mvc/webhooks.js
A config/plugins/webhooks/topbar_test/config/topbar_test.yml
M lib/galaxy/webhooks/__init__.py
A static/maps/mvc/webhooks.js.map
A static/scripts/mvc/webhooks.js
Log Message:
-----------
topbar webhooks testing
Commit: 17440d7b11b5013e52033efe4668115a466115b0
https://github.com/galaxyproject/galaxy/commit/17440d7b11b5013e52033efe4668…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A config/plugins/plugin1.xml
A config/plugins/plugin2.xml
A config/plugins/webhooks/plugin1/config/plugin1.yaml
A config/plugins/webhooks/plugin2/config/plugin2.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
add Webhooks draft
Commit: 143a740dc38fec9f92211d26364cb0b40235a24e
https://github.com/galaxyproject/galaxy/commit/143a740dc38fec9f92211d26364c…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R config/plugins/plugin1.xml
R config/plugins/plugin2.xml
Log Message:
-----------
remove extra files
Commit: 117c5263acdfb8853cc6771810ef87c755b006ce
https://github.com/galaxyproject/galaxy/commit/117c5263acdfb8853cc6771810ef…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/tool/tool-webhooks.js
M config/plugins/webhooks/plugin2/config/plugin2.yml
A config/plugins/webhooks/plugin2/static/style.css
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
add very basic plugin system (for tools)
Commit: ed2282d60b3f41c653e61be13d24ace6e83215ca
https://github.com/galaxyproject/galaxy/commit/ed2282d60b3f41c653e61be13d24…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin2/config/plugin2.yml
R config/plugins/webhooks/plugin2/static/style.css
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
add first webhook
Commit: 29129463a0be1778c69fce6e783dd75da05d53c0
https://github.com/galaxyproject/galaxy/commit/29129463a0be1778c69fce6e783d…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin1/config/plugin1.yaml
Log Message:
-----------
add one more plugin
Commit: 411674521cf1d9d3c5479ae334fbead783d737fe
https://github.com/galaxyproject/galaxy/commit/411674521cf1d9d3c5479ae334fb…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
topbar webhooks testing
Commit: b215de947c007dfc84ae4325d1a6b0be846986b5
https://github.com/galaxyproject/galaxy/commit/b215de947c007dfc84ae4325d1a6…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
A config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
R config/plugins/webhooks/topbar_test/config/topbar_test.yml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
renamings and fixes
Commit: bb9dc0560ade3f44037a4d03a24651b91af36dbd
https://github.com/galaxyproject/galaxy/commit/bb9dc0560ade3f44037a4d03a246…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/masthead_test/static/script.js
M config/plugins/webhooks/phdcomics/helper/__init__.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
- unify webhooks entry point
- simlify webhooks code (on load)
- improve code readability
- clean up
Commit: e95392b4b62b5ff803390287d0eac4f385504ef1
https://github.com/galaxyproject/galaxy/commit/e95392b4b62b5ff803390287d0ea…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
- add new entry point (Workflow)
- temporarily hide masthead webhook (due to instability)
Commit: f3b1232bdb46e9ccb4f27b3a1fc668d987d650cc
https://github.com/galaxyproject/galaxy/commit/f3b1232bdb46e9ccb4f27b3a1fc6…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/webhooks.js
A config/plugins/webhooks/history_test1/config/history_test1.yml
A config/plugins/webhooks/history_test2/config/history_test2.yml
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
add new entry point for History Panel menu
Commit: 578bdf679f0575e98922ddea004248de9b8b965c
https://github.com/galaxyproject/galaxy/commit/578bdf679f0575e98922ddea0042…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/history_test1/config/history_test1.yml
M config/plugins/webhooks/history_test2/config/history_test2.yml
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webhooks/__init__.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
bug fixes and improvements
Commit: 42adc9c7dfa1485162b78742f5ac3a7e8935902f
https://github.com/galaxyproject/galaxy/commit/42adc9c7dfa1485162b78742f5ac…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A config/plugins/plugin1.xml
A config/plugins/plugin2.xml
A config/plugins/webhooks/plugin1/config/plugin1.yaml
A config/plugins/webhooks/plugin2/config/plugin2.yml
Log Message:
-----------
add Webhooks draft
Commit: 6bc57ec0209f22970c4303870ba48cfea528e0ff
https://github.com/galaxyproject/galaxy/commit/6bc57ec0209f22970c4303870ba4…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R config/plugins/plugin1.xml
R config/plugins/plugin2.xml
Log Message:
-----------
remove extra files
Commit: ca769ab848209be8e4e48a6b28c13ecf52744e0f
https://github.com/galaxyproject/galaxy/commit/ca769ab848209be8e4e48a6b28c1…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/tool/tool-webhooks.js
M config/plugins/webhooks/plugin2/config/plugin2.yml
A config/plugins/webhooks/plugin2/static/style.css
Log Message:
-----------
add very basic plugin system (for tools)
Commit: 1a8a82370bcfd157f1d82ee6f6634bfcbcfb62af
https://github.com/galaxyproject/galaxy/commit/1a8a82370bcfd157f1d82ee6f663…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin2/config/plugin2.yml
R config/plugins/webhooks/plugin2/static/style.css
M config/plugins/webhooks/xkcd/config/xkcd.yml
Log Message:
-----------
add first webhook
Commit: 454a88b45174cfddae5ad79c31d92edffb07cabe
https://github.com/galaxyproject/galaxy/commit/454a88b45174cfddae5ad79c31d9…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin1/config/plugin1.yaml
Log Message:
-----------
add one more plugin
Commit: 53f56c3426714b3531dd1c49ecca431f73b77de9
https://github.com/galaxyproject/galaxy/commit/53f56c3426714b3531dd1c49ecca…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/tool/tool-webhooks.js
A config/plugins/webhooks/topbar_test/config/topbar_test.yml
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
topbar webhooks testing
Commit: c7f35c41d72a6131bfd0a4a7b3525518ed29d78a
https://github.com/galaxyproject/galaxy/commit/c7f35c41d72a6131bfd0a4a7b352…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A config/plugins/plugin1.xml
A config/plugins/plugin2.xml
A config/plugins/webhooks/plugin1/config/plugin1.yaml
A config/plugins/webhooks/plugin2/config/plugin2.yml
Log Message:
-----------
add Webhooks draft
Commit: a73d00fc04695b1f27a3cdf6091d352ee61f8f45
https://github.com/galaxyproject/galaxy/commit/a73d00fc04695b1f27a3cdf6091d…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R config/plugins/plugin1.xml
R config/plugins/plugin2.xml
Log Message:
-----------
remove extra files
Commit: 2b2be226ee9425742e0a629459e126b0c90e5e86
https://github.com/galaxyproject/galaxy/commit/2b2be226ee9425742e0a629459e1…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/tool/tool-webhooks.js
M config/plugins/webhooks/plugin2/config/plugin2.yml
A config/plugins/webhooks/plugin2/static/style.css
Log Message:
-----------
add very basic plugin system (for tools)
Commit: 211491fdf31a814590250edd4447916a5213120b
https://github.com/galaxyproject/galaxy/commit/211491fdf31a814590250edd4447…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin2/config/plugin2.yml
R config/plugins/webhooks/plugin2/static/style.css
Log Message:
-----------
add first webhook
Commit: 060df24ff5b329c37103f9c90caf65c4889c964d
https://github.com/galaxyproject/galaxy/commit/060df24ff5b329c37103f9c90caf…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-webhooks.js
R config/plugins/webhooks/plugin1/config/plugin1.yaml
Log Message:
-----------
add one more plugin
Commit: 00cf0cb85ec2cca9091de22fcaa6579d611530f1
https://github.com/galaxyproject/galaxy/commit/00cf0cb85ec2cca9091de22fcaa6…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R client/galaxy/scripts/mvc/tool/tool-webhooks.js
Log Message:
-----------
topbar webhooks testing
Commit: 27e0302ea3926e0a3ce6955317f6d1f38bc6f8b4
https://github.com/galaxyproject/galaxy/commit/27e0302ea3926e0a3ce6955317f6…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
R config/plugins/webhooks/topbar_test/config/topbar_test.yml
M config/plugins/webhooks/xkcd/config/xkcd.yml
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
renamings and fixes
Commit: 29a57ba0fdd9ab066e19110715bbb091014e3f7a
https://github.com/galaxyproject/galaxy/commit/29a57ba0fdd9ab066e19110715bb…
Author: anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M config/plugins/webhooks/xkcd/config/xkcd.yml
Log Message:
-----------
- add new entry point (Workflow)
- temporarily hide masthead webhook (due to instability)
Commit: e58fe7ca49f7b01244d1e6f4bfc92586459c799d
https://github.com/galaxyproject/galaxy/commit/e58fe7ca49f7b01244d1e6f4bfc9…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M config/plugins/webhooks/xkcd/config/xkcd.yml
Log Message:
-----------
bug fixes and improvements
Commit: 8b5716ddfda7d8d4bc604cf6d396d59fa45498c7
https://github.com/galaxyproject/galaxy/commit/8b5716ddfda7d8d4bc604cf6d396…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M config/plugins/webhooks/xkcd/config/xkcd.yml
M static/maps/mvc/webhooks.js.map
Log Message:
-----------
fix bugs after previous commit
Commit: ce346b6ad4482a1e6a0e8e9f92e79ea1d90a33b4
https://github.com/galaxyproject/galaxy/commit/ce346b6ad4482a1e6a0e8e9f92e7…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/webhooks.js
M config/plugins/webhooks/masthead_test/config/masthead_test.yml
R config/plugins/webhooks/masthead_test/static/script.js
M config/plugins/webhooks/phdcomics/helper/__init__.py
M static/maps/mvc/webhooks.js.map
M static/scripts/mvc/webhooks.js
Log Message:
-----------
pass trans object into the helper function
Commit: 2cc133f32507cd2aec8784e247106cef540a1c17
https://github.com/galaxyproject/galaxy/commit/2cc133f32507cd2aec8784e24710…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
A doc/source/admin/webhooks.rst
Log Message:
-----------
Add initial docs
Commit: 69a9344c529e34cdb70fdd71634ba2944bf0a7e8
https://github.com/galaxyproject/galaxy/commit/69a9344c529e34cdb70fdd71634b…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
A config/plugins/webhooks/trans_object/config/trans_object.yaml
A config/plugins/webhooks/trans_object/helper/__init__.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webhooks/__init__.py
M static/maps/layout/menu.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
- show Webhook on a workflow page
- fix merge errors
Commit: ef304a2223ca080c9181fad4117919c71d539211
https://github.com/galaxyproject/galaxy/commit/ef304a2223ca080c9181fad41179…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/layout/menu.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form.js
A templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
- merge
Commit: a3627b98ab8f5940af529e1387c8da8a4595a9e0
https://github.com/galaxyproject/galaxy/commit/a3627b98ab8f5940af529e1387c8…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-09 (Sun, 09 Oct 2016)
Changed paths:
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
Log Message:
-----------
make client
Commit: ad0d0bc7cec7c281052610b9453db42cfce8dcea
https://github.com/galaxyproject/galaxy/commit/ad0d0bc7cec7c281052610b9453d…
Author: ramezrawas <ramezrawas(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Missing double quotation
line 3664: name="output_vcf>
Commit: 217854827ac7dfc88c5388cd2ecb24fffd86c060
https://github.com/galaxyproject/galaxy/commit/217854827ac7dfc88c5388cd2ecb…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3027 from ramezrawas/patch-1
Missing double quotation
Commit: 4b5114bed1c09c655654972b084274e74310ebe8
https://github.com/galaxyproject/galaxy/commit/4b5114bed1c09c655654972b0842…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
A doc/source/admin/mulled_containers.rst
Log Message:
-----------
Merge pull request #50 from jmchilton/mulled_docs
Add initial documentation about the new mulled features.
Commit: fad562876f886e3384fec1a9782685251d12e2c1
https://github.com/galaxyproject/galaxy/commit/fad562876f886e3384fec1a97826…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Datatypes: include base classes in search by name
Fixes #2982
Adds the base class 'images.Image' to the list of classes
returnable by 'datatypes_registry.get_datatype_class_by_name'.
Normally that method searches the registry's list of datatypes and
those are instantiable classes only. The images.Image can be
considered an abstract base class and you'd never create a dataset
of that datatype.
The method is used for getting classes for 'isinstance' tests, however,
so including base classes like 'images.Image' allow testing for all
its image subclasses. This change makes that possible and allows the
method (and its consumers) to behave in a much more predictable and
useful manner.
Commit: 91bfecea67b78f7e459a250a7844c6344154367f
https://github.com/galaxyproject/galaxy/commit/91bfecea67b78f7e459a250a7844…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Add documentation on optional ``multiple="true"`` data parameters.
Thanks to detailed biostar question from @lindenb (sorry these parameters are so counter-intuitive - I don't have an excuse other than a need to preserve backward compatibility).
Rebased with indention requested by @nsoranzo and fixes for the test case tool.
Commit: f0b988da78f081bf6845ce2d280d153e221f3633
https://github.com/galaxyproject/galaxy/commit/f0b988da78f081bf6845ce2d280d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/util.py
Log Message:
-----------
Bring in latest galaxy-lib fixes.
Commit: 1e32c0926ca3fcee79f355577c5525c4bf73c8e4
https://github.com/galaxyproject/galaxy/commit/1e32c0926ca3fcee79f355577c55…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/style/source_material/circle.py
M doc/parse_gx_xsd.py
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
Log Message:
-----------
Fix import order and Python3 compatibility for most of test/
Commit: 20dcc4d693ae8fa7e846eb32e65292c3c4a38863
https://github.com/galaxyproject/galaxy/commit/20dcc4d693ae8fa7e846eb32e652…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
remove duplicated option from config sample
Commit: bcabbd8707e0064e041e730e5abd1d8dfc0a692c
https://github.com/galaxyproject/galaxy/commit/bcabbd8707e0064e041e730e5abd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M doc/source/admin/mulled_containers.rst
Log Message:
-----------
minor changes to mulled admin docs
Commit: 7db241faa6d505427108c5ddeae8dbc77c384613
https://github.com/galaxyproject/galaxy/commit/7db241faa6d505427108c5ddeae8…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A doc/source/admin/mulled_containers.rst
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Merge pull request #2986 from jmchilton/mulled
Implement beta support for discovering mulled containers for dependencies.
Commit: 1a2d75fade1077359b2a9b1072feab793022b7f4
https://github.com/galaxyproject/galaxy/commit/1a2d75fade1077359b2a9b1072fe…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M doc/source/admin/index.rst
Log Message:
-----------
add muled docs to admin index
Commit: 7d642c063f18b18b438a4840705f09652f3b586d
https://github.com/galaxyproject/galaxy/commit/7d642c063f18b18b438a4840705f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M doc/source/admin/index.rst
Log Message:
-----------
Merge pull request #3032 from martenson/link-mulled-docs
add muled docs to admin index
Commit: 75d1f8496acc060e8bd91cdaffd082fc9685ef1f
https://github.com/galaxyproject/galaxy/commit/75d1f8496acc060e8bd91cdaffd0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/style/source_material/circle.py
M doc/parse_gx_xsd.py
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
Log Message:
-----------
Merge pull request #3031 from nsoranzo/flake8-import-order
Fix import order and Python3 compatibility for most of test/
Commit: 191bae9a2b9d06bb7d461633b0a43ce320a042c4
https://github.com/galaxyproject/galaxy/commit/191bae9a2b9d06bb7d461633b0a4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-10 (Mon, 10 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/registry.py
Log Message:
-----------
Merge pull request #3028 from carlfeberhard/fix.tiff
Datatypes: include base classes in search by name
Commit: bf5cc30b843838f30a4b40faa9834cbc28a01991
https://github.com/galaxyproject/galaxy/commit/bf5cc30b843838f30a4b40faa983…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
R config/plugins/visualizations/charts/sample.txt
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Remove tabular file from repo, fix comments
Commit: 6639a181df3ba8f2a26e6a9bde27e53866cf110a
https://github.com/galaxyproject/galaxy/commit/6639a181df3ba8f2a26e6a9bde27…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #3025 from mvdbeek/cache_fix
Cache fix
Commit: 1156006733001fb06520a70f54a9227f5b4c7061
https://github.com/galaxyproject/galaxy/commit/1156006733001fb06520a70f54a9…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M .travis.yml
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
Log Message:
-----------
Merge branch 'release_16.07' into dev
Conflicts:
lib/galaxy/tools/deps/__init__.py
Commit: d93cedef8a3e727bc0a089ad6eda4c5734cd55c7
https://github.com/galaxyproject/galaxy/commit/d93cedef8a3e727bc0a089ad6eda…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Increase min number of columns for pileup sniffing to 5
Fix #3001.
Commit: 3be66005dc4cbd2a7d45e2a482f297dcaf493c02
https://github.com/galaxyproject/galaxy/commit/3be66005dc4cbd2a7d45e2a482f2…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Check that chromosome number is >=0
Commit: 1288cf0505eea6139bf9f34d60e6b255268d717d
https://github.com/galaxyproject/galaxy/commit/1288cf0505eea6139bf9f34d60e6…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Add workflow save-as functionality. Issue 3000
Commit: 2ab0b18706dc54cde3507e194a935f513c68119c
https://github.com/galaxyproject/galaxy/commit/2ab0b18706dc54cde3507e194a93…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Allow names with spaces
Commit: 2b9281a37832346b0a3e5aed1b13ee84270ffe44
https://github.com/galaxyproject/galaxy/commit/2b9281a37832346b0a3e5aed1b13…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Fix dependency ordering broken in #2917.
We will store dependencies in an OrderedDict, matching the order of `<requirements>`.
Fixes an issue where an R library was being sourced before R itself during shell command generation, the sourcing of R afterwards overwrote the `R_LIBS` env setting.
Commit: 58d608b9060d7608c33d711183790e3b19c313cc
https://github.com/galaxyproject/galaxy/commit/58d608b9060d7608c33d71118379…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Merge pull request #3036 from blankenberg/fix-dep-shell-order
Fix dependency ordering broken in #2917.
Commit: 1805ac8b5948ded11e154c887a2da99481ac70c6
https://github.com/galaxyproject/galaxy/commit/1805ac8b5948ded11e154c887a2d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
A config/plugins/visualizations/charts/static/client/app.css
A config/plugins/visualizations/charts/static/client/app.js
A config/plugins/visualizations/charts/static/client/components/model.js
A config/plugins/visualizations/charts/static/client/components/screenshot.js
A config/plugins/visualizations/charts/static/client/views/description.js
A config/plugins/visualizations/charts/static/client/views/editor.js
A config/plugins/visualizations/charts/static/client/views/groups.js
A config/plugins/visualizations/charts/static/client/views/settings.js
A config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/client/views/viewer.js
A config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
A config/plugins/visualizations/charts/static/repository/build/others_example.js
A config/plugins/visualizations/charts/static/repository/build/others_example.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.js
A config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
Log Message:
-----------
Add chart plugins back to plugins directory of visualization framework
Commit: f467384fdd97dba43ee0f9b7c3592498de738ee8
https://github.com/galaxyproject/galaxy/commit/f467384fdd97dba43ee0f9b7c359…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Use fixed repository path
Commit: fe73009db5248a04844db86584064b48a86f2cb2
https://github.com/galaxyproject/galaxy/commit/fe73009db5248a04844db8658406…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/static/client/components/model.js
Log Message:
-----------
Fix default options for storing request
Commit: cc36793cd0d249fd2794c5de54af6ff10695b88e
https://github.com/galaxyproject/galaxy/commit/cc36793cd0d249fd2794c5de54af…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/webhooks.js
M lib/galaxy/webapps/galaxy/api/webhooks.py
M static/maps/layout/menu.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
- remove separate functions for adding masthead/history-menu plugins
- choose a random tool/workflow plugin only among active ones
Commit: 812aca5b34df584a09d3f82f9d938e89d396b2bd
https://github.com/galaxyproject/galaxy/commit/812aca5b34df584a09d3f82f9d93…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/webhooks.py
Log Message:
-----------
bug fix
Commit: 5f9154a6179f194a8186d0f91a375d449cb26ea2
https://github.com/galaxyproject/galaxy/commit/5f9154a6179f194a8186d0f91a37…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
tiny fixes
Commit: cd92be8802e520a2f53eceb385f018ded4aea218
https://github.com/galaxyproject/galaxy/commit/cd92be8802e520a2f53eceb385f0…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Include a section about plugin dependencies.
Commit: 0ad7c99ea20ba49725fffe5a356ab39bf601111d
https://github.com/galaxyproject/galaxy/commit/0ad7c99ea20ba49725fffe5a356a…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Extended the documentation of webhooks and added an images directory.
Commit: f29b003a8cd6a277ee67cb553653063fbc53dbfe
https://github.com/galaxyproject/galaxy/commit/f29b003a8cd6a277ee67cb553653…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
A doc/source/admin/images_webhooks/history-menu.png
A doc/source/admin/images_webhooks/masthead.png
A doc/source/admin/images_webhooks/masthead_trans_object.png
A doc/source/admin/images_webhooks/tool.png
A doc/source/admin/images_webhooks/workflow.png
Log Message:
-----------
Added images directory for webhooks documentation
Commit: 95c1f186935a77ee71de59a3a616dc5d7f11c8c2
https://github.com/galaxyproject/galaxy/commit/95c1f186935a77ee71de59a3a616…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixed formatting errors
Commit: eb32ad229f5f22c8b2cb497344fd545f14f6eae3
https://github.com/galaxyproject/galaxy/commit/eb32ad229f5f22c8b2cb497344fd…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixed formatting errors
Commit: d1737110bf2d870346df43d5969b329cea1b16d8
https://github.com/galaxyproject/galaxy/commit/d1737110bf2d870346df43d5969b…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: 76b9e004d204b6569ef6d19b6e808b77db9984f2
https://github.com/galaxyproject/galaxy/commit/76b9e004d204b6569ef6d19b6e80…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: 8030d2025ddaa0ca5f5d58f12a24f85e860f9339
https://github.com/galaxyproject/galaxy/commit/8030d2025ddaa0ca5f5d58f12a24…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: acd99f76fc967445cc9b8cd1317793a6074997b7
https://github.com/galaxyproject/galaxy/commit/acd99f76fc967445cc9b8cd13177…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: 6684fd4e262f97c313d907bf44409d94172338c8
https://github.com/galaxyproject/galaxy/commit/6684fd4e262f97c313d907bf4440…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: fafeedc286035d78d1033220717b346e4c0d3c99
https://github.com/galaxyproject/galaxy/commit/fafeedc286035d78d1033220717b…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: af8a3f11048c86f91f17044344211a5cdba98b13
https://github.com/galaxyproject/galaxy/commit/af8a3f11048c86f91f1704434421…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Fixing errors
Commit: dcde64ce407b332072525c66885adf03a26eeb5e
https://github.com/galaxyproject/galaxy/commit/dcde64ce407b332072525c66885a…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/workflow/extract.py
M test/api/test_workflow_extraction.py
Log Message:
-----------
Fix import order. Fix typos and improve readability
Commit: 04bf2153b8f61c60288cb180d448e7c20352f6e7
https://github.com/galaxyproject/galaxy/commit/04bf2153b8f61c60288cb180d448…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M lib/galaxy/workflow/extract.py
Log Message:
-----------
WorkflowSummary: add dict to map a job id to its representative job
Fix #2742 introduced in commit 9ede8e556be1f6038361b579c1457068e50e951a .
The representative job is the first in the returned query, so substantially
random and not necessarily the one with the lowest job id.
Mapping a job id to its representative job in extract_steps() makes it
robust also against API requests with manually chosen collection job ids.
Commit: d5dc39ab0f034d79252a9fb0875824cbf8b02e04
https://github.com/galaxyproject/galaxy/commit/d5dc39ab0f034d79252a9fb08758…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
A doc/source/admin/images_webhooks/history-menu.png
A doc/source/admin/images_webhooks/masthead.png
A doc/source/admin/images_webhooks/masthead_trans_object.png
A doc/source/admin/images_webhooks/tool.png
A doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/webhooks.rst
Log Message:
-----------
Merge pull request #21 from joachimwolff/feature/plugin-system
Feature/plugin system
Commit: 0a15289d31a189df71490bba5392726ac0f6db47
https://github.com/galaxyproject/galaxy/commit/0a15289d31a189df71490bba5392…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M config/plugins/webhooks/phdcomics/helper/__init__.py
Log Message:
-----------
added missing dependencies check
Commit: bc51dc3ec72dc7a5bbcc42bcd4f1cc834c1a69b6
https://github.com/galaxyproject/galaxy/commit/bc51dc3ec72dc7a5bbcc42bcd4f1…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Update webhooks.rst
escape missing dependencies
Commit: 95d6990cf3f6f1e4ade87b6ba6557c99471ff924
https://github.com/galaxyproject/galaxy/commit/95d6990cf3f6f1e4ade87b6ba655…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Update webhooks.rst
Commit: 4f89528c94d33f1e3eca8df9dd34c06965e7beec
https://github.com/galaxyproject/galaxy/commit/4f89528c94d33f1e3eca8df9dd34…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
make activation procedure more clear
Commit: 1e2688f1578552ea03e7a601d927c4475b96fdd2
https://github.com/galaxyproject/galaxy/commit/1e2688f1578552ea03e7a601d927…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #3024 from jmchilton/multi_optional_param
Add documentation on optional ``multiple="true"`` data parameters.
Commit: c6713e7c31d5ffe576af5af7de56d3536d196786
https://github.com/galaxyproject/galaxy/commit/c6713e7c31d5ffe576af5af7de56…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-12 (Wed, 12 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/workflow/extract.py
M test/api/test_workflow_extraction.py
Log Message:
-----------
Merge pull request #3039 from nsoranzo/fix_for_2742
Fix workflow extraction API tests on PostgreSQL
Commit: 2d915a42f6329bd31dfdc76b5bfa56376a57c841
https://github.com/galaxyproject/galaxy/commit/2d915a42f6329bd31dfdc76b5bfa…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
tense changes
Commit: 77f78cfbc79ddc345bc22277afc335f11e189491
https://github.com/galaxyproject/galaxy/commit/77f78cfbc79ddc345bc22277afc3…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/driver_util.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
Log Message:
-----------
Change __all__ from list to tuple
Also fix import order and Python3 compatibility.
Commit: bb4428896839898fb5d0c9b88ae18fc9b705a27b
https://github.com/galaxyproject/galaxy/commit/bb4428896839898fb5d0c9b88ae1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/util/checkers.py
M tools/data_source/upload.py
Log Message:
-----------
Failthrough to using imghdr when PIL does not detect an image correctly.
Some misc cleanup, avoiding use of system functions as variable names,
etc.
Commit: cb6e25278c4a59d4ea2edd9ce5e9c757b1ebf7f8
https://github.com/galaxyproject/galaxy/commit/cb6e25278c4a59d4ea2edd9ce5e9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/image_util.py
M tools/data_source/upload.py
Log Message:
-----------
Refactoring, because it was bugging me.
Commit: ba07956117e5e4527fa5d2837da2c267f6ab981d
https://github.com/galaxyproject/galaxy/commit/ba07956117e5e4527fa5d2837da2…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M tools/stats/filtering.py
Log Message:
-----------
Fix tabular filtering tool broken in #2983
Commit: 5d294ea7d3a14561a15c30f3527dfcd21d517369
https://github.com/galaxyproject/galaxy/commit/5d294ea7d3a14561a15c30f3527d…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
Log Message:
-----------
Fix GFF attribute filtering tool broken in #2983
Commit: 32bc17cdaa636ba0ba2a97a372b37d518cdd6390
https://github.com/galaxyproject/galaxy/commit/32bc17cdaa636ba0ba2a97a372b3…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
Log Message:
-----------
Whitespace fix
Commit: b6d4473aa0975f88b2d2cf8aa1372aecfc92919b
https://github.com/galaxyproject/galaxy/commit/b6d4473aa0975f88b2d2cf8aa137…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix for displaying parameters to the user, that have a False value.
Previously, e.g. an integer with a value of 0 would display "Not available.".
Commit: ed263bf8a52b37199cc7822126598a75a9984335
https://github.com/galaxyproject/galaxy/commit/ed263bf8a52b37199cc782212659…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/util/image_util.py
Log Message:
-----------
import order.
Commit: 4bc429776853239961c45c9656c69b3be0ae01bc
https://github.com/galaxyproject/galaxy/commit/4bc429776853239961c45c9656c6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/util/image_util.py
Log Message:
-----------
Simplify, strip out passing of image.
Commit: 6c17d1a823b4367b93fff61d7f2fbed23dc5de3b
https://github.com/galaxyproject/galaxy/commit/6c17d1a823b4367b93fff61d7f2f…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Remove outdated warning
After digging through the code I am not finding evidence that this
was ever possible to do, at least not since sometime pre-2010.
Commit: a22a4d0bd5a2376c130ad84e4bc0313b9f252e45
https://github.com/galaxyproject/galaxy/commit/a22a4d0bd5a2376c130ad84e4bc0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Merge pull request #3046 from erasche/remove_warning
Remove outdated warning on ID_SECRET
Commit: 36ae57c6e028fc814af1cd4740e9222dfcb56021
https://github.com/galaxyproject/galaxy/commit/36ae57c6e028fc814af1cd4740e9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M tools/stats/filtering.py
Log Message:
-----------
Merge pull request #3043 from blankenberg/fix-filter-tool
Fix tabular filtering tool broken in #2983
Commit: f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461
https://github.com/galaxyproject/galaxy/commit/f6d5f3c4a2e51bd6b75a99dc0153…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix downloading tool tarball with boolean test input values.
Commit: b52d5be75b3f2bf9cae86d4a278689cb614095be
https://github.com/galaxyproject/galaxy/commit/b52d5be75b3f2bf9cae86d4a2786…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Change according to Aysam's review
Commit: 290c48b16c54fab54ec35601e04d6877071a78db
https://github.com/galaxyproject/galaxy/commit/290c48b16c54fab54ec35601e04d…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Change according to Aysam's review
Commit: a231e240ed1a8002318678dde5979c3febb11770
https://github.com/galaxyproject/galaxy/commit/a231e240ed1a8002318678dde597…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
remove obsolete code
Commit: 6a62dbc91a0f2ed282c2cc1e3c4227faed870ace
https://github.com/galaxyproject/galaxy/commit/6a62dbc91a0f2ed282c2cc1e3c42…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M doc/parse_gx_xsd.py
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Merge branch 'dev' into feature/plugin-system
Commit: 8f5b54141dd2b46d3b532915b082c4bd5eeff44c
https://github.com/galaxyproject/galaxy/commit/8f5b54141dd2b46d3b532915b082…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
code optimization, thanks Sam
Commit: 773d85453f965712cdd8bcc209b9a05897959994
https://github.com/galaxyproject/galaxy/commit/773d85453f965712cdd8bcc209b9…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
A config/plugins/webhooks/demo/history_test1/config/history_test1.yml
A config/plugins/webhooks/demo/history_test2/config/history_test2.yml
A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml
A config/plugins/webhooks/demo/phdcomics/helper/__init__.py
A config/plugins/webhooks/demo/phdcomics/static/script.js
A config/plugins/webhooks/demo/phdcomics/static/styles.css
A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml
A config/plugins/webhooks/demo/trans_object/helper/__init__.py
A config/plugins/webhooks/demo/xkcd/config/xkcd.yml
A config/plugins/webhooks/demo/xkcd/static/script.js
A config/plugins/webhooks/demo/xkcd/static/styles.css
R config/plugins/webhooks/history_test1/config/history_test1.yml
R config/plugins/webhooks/history_test2/config/history_test2.yml
R config/plugins/webhooks/masthead_test/config/masthead_test.yml
R config/plugins/webhooks/phdcomics/config/phdcomics.yaml
R config/plugins/webhooks/phdcomics/helper/__init__.py
R config/plugins/webhooks/phdcomics/static/script.js
R config/plugins/webhooks/phdcomics/static/styles.css
R config/plugins/webhooks/trans_object/config/trans_object.yaml
R config/plugins/webhooks/trans_object/helper/__init__.py
R config/plugins/webhooks/xkcd/config/xkcd.yml
R config/plugins/webhooks/xkcd/static/script.js
R config/plugins/webhooks/xkcd/static/styles.css
Log Message:
-----------
move all plugins into a demo folder
Commit: 277727ada67d32404dc953d393716af8aa2aabdc
https://github.com/galaxyproject/galaxy/commit/277727ada67d32404dc953d39371…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/driver_util.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
Log Message:
-----------
Merge pull request #3041 from nsoranzo/flake8-import-order
Change __all__ from list to tuple [1/2]
Commit: a676d6e8234dd9db59376df7f54633a78e503f86
https://github.com/galaxyproject/galaxy/commit/a676d6e8234dd9db59376df7f546…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
allow multiple webhook dirs
Commit: 0062eacfdf86fbfe8fda3de88b2b5b122cdc567e
https://github.com/galaxyproject/galaxy/commit/0062eacfdf86fbfe8fda3de88b2b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
Log Message:
-----------
Merge pull request #3044 from blankenberg/gff-filter-tool-fix
Fix GFF attribute filtering tool broken in #2983
Commit: 6894df3dcb0f308724331bceceff46dba23156a1
https://github.com/galaxyproject/galaxy/commit/6894df3dcb0f308724331bceceff…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/layout/menu.js
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/plugins/webhooks/demo/history_test1/config/history_test1.yml
A config/plugins/webhooks/demo/history_test2/config/history_test2.yml
A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml
A config/plugins/webhooks/demo/phdcomics/helper/__init__.py
A config/plugins/webhooks/demo/phdcomics/static/script.js
A config/plugins/webhooks/demo/phdcomics/static/styles.css
A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml
A config/plugins/webhooks/demo/trans_object/helper/__init__.py
A config/plugins/webhooks/demo/xkcd/config/xkcd.yml
A config/plugins/webhooks/demo/xkcd/static/script.js
A config/plugins/webhooks/demo/xkcd/static/styles.css
R config/plugins/webhooks/history_test1/config/history_test1.yml
R config/plugins/webhooks/history_test2/config/history_test2.yml
R config/plugins/webhooks/masthead_test/config/masthead_test.yml
R config/plugins/webhooks/phdcomics/config/phdcomics.yaml
R config/plugins/webhooks/phdcomics/helper/__init__.py
R config/plugins/webhooks/phdcomics/static/script.js
R config/plugins/webhooks/phdcomics/static/styles.css
R config/plugins/webhooks/trans_object/config/trans_object.yaml
R config/plugins/webhooks/trans_object/helper/__init__.py
R config/plugins/webhooks/xkcd/config/xkcd.yml
R config/plugins/webhooks/xkcd/static/script.js
R config/plugins/webhooks/xkcd/static/styles.css
M doc/parse_gx_xsd.py
M doc/source/admin/dependency_resolvers.rst
A doc/source/admin/images_webhooks/history-menu.png
A doc/source/admin/images_webhooks/masthead.png
A doc/source/admin/images_webhooks/masthead_trans_object.png
A doc/source/admin/images_webhooks/tool.png
A doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/admin/webhooks.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/tools/deps/__init__.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webhooks/__init__.py
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/mulled_example_multi_1.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_runner_local.py
Log Message:
-----------
Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system
Commit: 3f8d45b388e5788b23c39c2b544e4c98eae8018f
https://github.com/galaxyproject/galaxy/commit/3f8d45b388e5788b23c39c2b544e…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
PEP8
Commit: fb516d9387a2df9a1ccdd2c7a1a1ce162f7e52fc
https://github.com/galaxyproject/galaxy/commit/fb516d9387a2df9a1ccdd2c7a1a1…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
remove blank line
Commit: b9e4bf58c5b656089ac8402632677503e6a86c65
https://github.com/galaxyproject/galaxy/commit/b9e4bf58c5b656089ac840263267…
Author: Lance Parsons <lparsons(a)princeton.edu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
Log Message:
-----------
Sort bedtools output in bam_to_bigwig conversion
Bedtools genomecov seems to output bedgraph files with chromosomes
sorted in the order given in the chromInfo file. This can cause issues
with bedGraphToBigWig which requires them sorted in a specific way.
Fixes #2582.
Commit: e220ed097067124f5ab616d0ece35d0af4cb2539
https://github.com/galaxyproject/galaxy/commit/e220ed097067124f5ab616d0ece3…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
use config_directories_from_setting
Commit: b0b5157f36ec26090c9c11c0a133513083015735
https://github.com/galaxyproject/galaxy/commit/b0b5157f36ec26090c9c11c0a133…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M config/plugins/webhooks/demo/phdcomics/helper/__init__.py
Log Message:
-----------
merge
Commit: f4dc38a54da3539f4d63f7e33708bcc2e33012fb
https://github.com/galaxyproject/galaxy/commit/f4dc38a54da3539f4d63f7e33708…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M config/plugins/webhooks/demo/history_test1/config/history_test1.yml
M config/plugins/webhooks/demo/history_test2/config/history_test2.yml
M config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml
M config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml
M config/plugins/webhooks/demo/trans_object/config/trans_object.yaml
M config/plugins/webhooks/demo/xkcd/config/xkcd.yml
Log Message:
-----------
activate all plugins in the demo folder
Commit: 2703ba1a0cc3a28314018299b8f1a686dfb6e995
https://github.com/galaxyproject/galaxy/commit/2703ba1a0cc3a28314018299b8f1…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
activate all demo plugins in testing purposes
Commit: afbea0dbfda0ad231a101aa0d7c25ee3822d9f7e
https://github.com/galaxyproject/galaxy/commit/afbea0dbfda0ad231a101aa0d7c2…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Present tool help from history entry. Issue 2100
Commit: 8694356ab7057c47164a92f8d4e47a800fca2f4d
https://github.com/galaxyproject/galaxy/commit/8694356ab7057c47164a92f8d4e4…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Adopt help to the latest changes
Commit: 3aadd84b80bca7fc588ffccaa27f01c1d599b9d8
https://github.com/galaxyproject/galaxy/commit/3aadd84b80bca7fc588ffccaa27f…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M config/plugins/webhooks/demo/trans_object/helper/__init__.py
Log Message:
-----------
add case where no user is logged in
Commit: 0dc2c95bd07e2a53dec27c8d0d4fc86747aa8878
https://github.com/galaxyproject/galaxy/commit/0dc2c95bd07e2a53dec27c8d0d4f…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Merge branch 'feature/plugin-system' of https://github.com/bgruening/galaxy into feature/plugin-system
Commit: 3cb8189e1fa48c58afaf609691a0801e784484b7
https://github.com/galaxyproject/galaxy/commit/3cb8189e1fa48c58afaf609691a0…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/galaxy.ini.sample
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M test/api/test_workflow_extraction.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/driver_util.py
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge branch 'dev' into feature/plugin-system
Commit: 4446ccc98c970f5077080f563585c90b1f84dc3a
https://github.com/galaxyproject/galaxy/commit/4446ccc98c970f5077080f563585…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #3045 from blankenberg/value_to_display_text-fix
Fix for displaying parameters to the user, that have a False value.
Commit: 37702392817107dfd12cbb54f0af1dcb18bd848e
https://github.com/galaxyproject/galaxy/commit/37702392817107dfd12cbb54f0af…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M config/galaxy.ini.sample
M config/plugins/webhooks/demo/trans_object/helper/__init__.py
M doc/source/admin/webhooks.rst
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M test/api/test_workflow_extraction.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/driver_util.py
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system
Commit: bd20ab1aa57381b36e16dc08c20b6b176a7ed724
https://github.com/galaxyproject/galaxy/commit/bd20ab1aa57381b36e16dc08c20b…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M lib/galaxy/webhooks/__init__.py
Log Message:
-----------
pep8
Commit: 3d4f302c4734e9afc7e065645c915dfd8f37566e
https://github.com/galaxyproject/galaxy/commit/3d4f302c4734e9afc7e065645c91…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
change default settings in galaxy.ini.sample
Commit: d26f46423e5d79dd8d0519d90350389838fece3c
https://github.com/galaxyproject/galaxy/commit/d26f46423e5d79dd8d0519d90350…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/image_util.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #3042 from dannon/image_detection_fixes
Image detection fixes
Commit: 4bbab51c0500922c9a191d022de295daa48f0dd5
https://github.com/galaxyproject/galaxy/commit/4bbab51c0500922c9a191d022de2…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
Add note about interface stability.
Commit: e5913a49e260be47ff4f32ae21780264731d98d5
https://github.com/galaxyproject/galaxy/commit/e5913a49e260be47ff4f32ae2178…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3047 from galaxyproject/tool_tarball_fix
Fix downloading tool tarball with boolean test input values.
Commit: 36134bca694c9dc6b2584fb661dfbce4ddb793e6
https://github.com/galaxyproject/galaxy/commit/36134bca694c9dc6b2584fb661df…
Author: Scott Szakonyi <sszakony(a)nd.edu>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
Log Message:
-----------
Added code to adjust top setting of tool search if messagebox is visible, issue 2907
Commit: 6312d8052b9668a03b3bb25ea02b9d42ac32de6d
https://github.com/galaxyproject/galaxy/commit/6312d8052b9668a03b3bb25ea02b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Rebuild cilent.
Commit: 28bb83f0ab5e93b5f961f12dac555bf96a9073ea
https://github.com/galaxyproject/galaxy/commit/28bb83f0ab5e93b5f961f12dac55…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tools.js
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Merge pull request #3055 from dannon/cherrypick_masthead_fix
Cherrypick masthead fix
Commit: a895c823daaf01c2b1b883dc256452411de9a728
https://github.com/galaxyproject/galaxy/commit/a895c823daaf01c2b1b883dc2564…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Merge pull request #3019 from blankenberg/collection-wf-resume-error
Fix for rerunning tool with workflow resume that is part of a collection.
Commit: 868658c7e72e3d0f37e36c51316a72a56a270376
https://github.com/galaxyproject/galaxy/commit/868658c7e72e3d0f37e36c51316a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Always display text, with test cases
Commit: f053f9bb3d2820c09aab1a0bc3b29e27eed56d09
https://github.com/galaxyproject/galaxy/commit/f053f9bb3d2820c09aab1a0bc3b2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M doc/parse_gx_xsd.py
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/checkers.py
A lib/galaxy/util/image_util.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_runner_local.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
M tools/data_source/upload.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: ebaffa2e0d6a030dfc3c78a3b9515093b14f7103
https://github.com/galaxyproject/galaxy/commit/ebaffa2e0d6a030dfc3c78a3b951…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M config/plugins/webhooks/demo/phdcomics/helper/__init__.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
Log Message:
-----------
fix failing Travis tests #2 (TOX_ENV=py27-lint) and #6 (TOX_ENV=py27-lint-imports)
Commit: 15ad14e6620706d6dbb39176783e274e01eebb3b
https://github.com/galaxyproject/galaxy/commit/15ad14e6620706d6dbb39176783e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-16 (Sun, 16 Oct 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Enhance merge collection work from @Takadonet with more merge conflict actions.
And allow it to work over any number of input collections.
Commit: 448a27a4a1ebe2b25b40eca11b7aa319f7345c61
https://github.com/galaxyproject/galaxy/commit/448a27a4a1ebe2b25b40eca11b7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-16 (Sun, 16 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A doc/parse_gx_xsd.py
A doc/schema_template.md
M doc/source/admin/chat.rst
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/api/guidelines.rst
M doc/source/project/issues.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/dockerfiles.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
R lib/galaxy/tools/toolbox/requirements.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/filelock.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
M setup.cfg
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/tests/form_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/utility.py
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into collection_tools
Commit: 49eac93882226e6f29624c676d593ae78719d7e5
https://github.com/galaxyproject/galaxy/commit/49eac93882226e6f29624c676d59…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-16 (Sun, 16 Oct 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
Log Message:
-----------
Cleanup merge collection and get test cases working again.
Commit: 7d938e2a23ca3ce8e3fac430bce494ce8f5238c3
https://github.com/galaxyproject/galaxy/commit/7d938e2a23ca3ce8e3fac430bce4…
Author: Philip Mabon <philipmabon(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A doc/parse_gx_xsd.py
A doc/schema_template.md
M doc/source/admin/chat.rst
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/api/guidelines.rst
M doc/source/project/issues.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/dockerfiles.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
R lib/galaxy/tools/toolbox/requirements.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/filelock.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
M setup.cfg
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/tests/form_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/utility.py
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge pull request #1 from jmchilton/collection_tools
Enhance the Merge Collections Tool
Commit: 31cb477e1a538c74360f039dda23907d0856adb6
https://github.com/galaxyproject/galaxy/commit/31cb477e1a538c74360f039dda23…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/filter_failed_collection.xml
A lib/galaxy/tools/merge_collection.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #2771 from Takadonet/dev
Collection Operator tools
Commit: 762337e110d7a8d4058d7fcc7fd41147b0d89020
https://github.com/galaxyproject/galaxy/commit/762337e110d7a8d4058d7fcc7fd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Fix import orders for updates to flake8_import_order.
Commit: 4bf1994fc3fd09b874c9ea29a8871269d44ad193
https://github.com/galaxyproject/galaxy/commit/4bf1994fc3fd09b874c9ea29a887…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Merge pull request #3059 from jmchilton/import_update
Fix import orders for updates to flake8_import_order.
Commit: 7207c15090385a397493da0503b06dbea1004d68
https://github.com/galaxyproject/galaxy/commit/7207c15090385a397493da0503b0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Merge pull request #3033 from nsoranzo/fix_for_3001
Increase min number of columns for pileup sniffing to 5
Commit: 22839eeee0b0909bc2726e60ffb26a213ddfc553
https://github.com/galaxyproject/galaxy/commit/22839eeee0b0909bc2726e60ffb2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #3052 from guerler/always_display_text
Always display text
Commit: 7eb413f4e8ee97d68a6fa466d9c5189b324dde52
https://github.com/galaxyproject/galaxy/commit/7eb413f4e8ee97d68a6fa466d9c5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M doc/schema_template.md
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Merge pull request #2961 from jmchilton/xsd_fixes_1
Improve ``version_command`` tag.
Commit: 1dc2d6a4ead34b9d8bdaecf85f146ca17b5e803c
https://github.com/galaxyproject/galaxy/commit/1dc2d6a4ead34b9d8bdaecf85f14…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/utils/utils.js
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
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A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/utils/utils.js
Log Message:
-----------
Merge pull request #2875 from guerler/remote_chart_plugins
Link charts to external repo, adjust interface
Commit: 3e737c99ea21dcb7ea3a326d36aee9c715c8d70b
https://github.com/galaxyproject/galaxy/commit/3e737c99ea21dcb7ea3a326d36ae…
Author: Remi Marenco <remi.marenco(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M .gitignore
M Makefile
M doc/source/conf.py
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/model/migrate/check.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
Log Message:
-----------
Add Galaxy Architecture slides in .md
+ the plumbing for slides creation
Init of #2244, second part: Python converter md to html + wip on GCC 2015 talk conversion
Add the 2. Galaxy app architecture. Need images
Add the 3. Galaxy components and object model
Add more content in md
Fix linting error by adding newline at the end of build_slideshow.py
Moved the galaxyArchitecture.md into a folder dedicated to it
Add 7th and 17th image + add style.css to have a better management of layout + added first slide as the first in GCC2015 slide
Set properly the CSS used in the whole presentation + add special to p and first slide
Add special orange for regular text and green emphasis (emphasis_2_galaxy)
Changed the font to PT Sans
Add 3. with images + few modifications
Removed the images integrated using background-image by now Markdown imaging (still need work, image's size seems not good by default
Add Makefile target to build architecture slides...
2016 Updates to 2015 architecture talk.
More intro slides for Galaxy architecture.
Update author line.
Progress on architecture slides...
- Improved styling (use Oxygen - closer to Galaxy font)
- Add ability to generate SVG diagrams to slide infrastructure
- Add newer client-server sequence diagram based on that.
Improved logging when there are problems with SQL migrations.
More misc work on architecture talk.
More images, slides, slide formatting, and initial work on an IPython notebook.
Improved styling for architecture slides...
Updates to architecture talk...
- Infrastructure for building class diagrams with plantuml
- Bring in move SVGs from last year's google docs.
- Fill out section on client architecture.
More work on slides for architecture talk.
Add startup_output.
Replace mermaid diagrams with plantuml diagrams.
Fill out these diagrams more and style them for a black background in Galaxy oranges.
Commit: 564aeeccd7379a5717de2180f5eb3208e479ea98
https://github.com/galaxyproject/galaxy/commit/564aeeccd7379a5717de2180f5eb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M Makefile
Log Message:
-----------
remove the duplicated variable
Commit: 32d0db8bb3b3b64a96beb1f09908cb1e3c1e3c28
https://github.com/galaxyproject/galaxy/commit/32d0db8bb3b3b64a96beb1f09908…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Job ID comes from creating_job value in dataset metadata.
Commit: bdc8829dd2363c759b362a275757448173afcd22
https://github.com/galaxyproject/galaxy/commit/bdc8829dd2363c759b362a275757…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/static/client/app.js
Log Message:
-----------
Dataset metadata should not be cached when building chart visualizations
Commit: 5a2d01b267398bb01620faeec0d665291ac953ad
https://github.com/galaxyproject/galaxy/commit/5a2d01b267398bb01620faeec0d6…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
Log Message:
-----------
Move help button to last position of left group, add 5px padding to help text.
Commit: 569723a4e5487c4eab25dfe619cda5b044b6115b
https://github.com/galaxyproject/galaxy/commit/569723a4e5487c4eab25dfe619cd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M .gitignore
M Makefile
M doc/source/conf.py
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/model/migrate/check.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
Log Message:
-----------
Merge pull request #3060 from martenson/remimarenco-gcc2015_talk
Add Galaxy Architecture slides in .md
Commit: a431d88293faf8f6286cae416f8842ce186692c4
https://github.com/galaxyproject/galaxy/commit/a431d88293faf8f6286cae416f88…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Add tool xml reload to tool run page - for admins only
Commit: 2a7e4f79c0c04158fe37dbd6c1b95cc251537173
https://github.com/galaxyproject/galaxy/commit/2a7e4f79c0c04158fe37dbd6c1b9…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/static/client/app.js
Log Message:
-----------
Merge pull request #3062 from guerler/fix_dataset_caching
Dataset metadata should not be cached when building chart visualizations
Commit: e4b3766c1b8798ab20a00c98d10f7bbf29da16ab
https://github.com/galaxyproject/galaxy/commit/e4b3766c1b8798ab20a00c98d10f…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/__init__.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/topsort.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/__init__.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M scripts/db_shell.py
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Change remaining __all__ from list to tuple
Also fix import order and Python3 compatibility.
Commit: 38464b5b284289c66263adc19afa0a6be2e24389
https://github.com/galaxyproject/galaxy/commit/38464b5b284289c66263adc19afa…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Originating workflow must be unchanged, load save as workflow to editor on save.
Commit: 3a99bbae0716c98aa8e8d290a666909ac88c0817
https://github.com/galaxyproject/galaxy/commit/3a99bbae0716c98aa8e8d290a666…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Add deprecated, legacy attribute default_value to XSD.
Cleanup use of ``gxdocs:deprecated``.
Commit: 69636f5e65e6b3ad2c8d7e3c300cd81418bb6206
https://github.com/galaxyproject/galaxy/commit/69636f5e65e6b3ad2c8d7e3c300c…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Add CEL file as a datatype
Commit: 7e2725d1250fef33d1d03cc4e15b29de6f1a540f
https://github.com/galaxyproject/galaxy/commit/7e2725d1250fef33d1d03cc4e15b…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
add CEL datatypes to datatypes conf sample
Commit: 05f792edcd4bf779d0e9c91f5f4c92396979f17b
https://github.com/galaxyproject/galaxy/commit/05f792edcd4bf779d0e9c91f5f4c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Specify actual parameter to use in lieu of default_value in XSD.
As suggested by @nsoranzo.
Commit: cfeb0135ac5fc3334d5a3afcfdfd1e586ce5d32f
https://github.com/galaxyproject/galaxy/commit/cfeb0135ac5fc3334d5a3afcfdfd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3072 from jmchilton/default_value_legacy_xsd
Add deprecated, legacy attribute default_value to XSD.
Commit: f9357ea07ddf0525b3a82021c9e11f690c700d67
https://github.com/galaxyproject/galaxy/commit/f9357ea07ddf0525b3a82021c9e1…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Add modal confirmation for tool reload.
Commit: 096a7bf94d799f905013f7052c1bdf87062a45a7
https://github.com/galaxyproject/galaxy/commit/096a7bf94d799f905013f7052c1b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
fix the incorrect handling of root when prefix is in play
Commit: b31bd5be35b207ce3be3c287c5fa7831a40986d7
https://github.com/galaxyproject/galaxy/commit/b31bd5be35b207ce3be3c287c5fa…
Author: tmcgowan <mcgo0092(a)umn.edu>
Date: 2016-10-21 (Fri, 21 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Extend PUT /api/workflows/{id} with additional workflow properties
Commit: a6d52cdbdc837c427c0971c6586eb5169a786752
https://github.com/galaxyproject/galaxy/commit/a6d52cdbdc837c427c0971c6586e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-23 (Sun, 23 Oct 2016)
Changed paths:
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
A client/galaxy/scripts/mvc/webhooks.js
M config/galaxy.ini.sample
A config/plugins/webhooks/demo/history_test1/config/history_test1.yml
A config/plugins/webhooks/demo/history_test2/config/history_test2.yml
A config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml
A config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml
A config/plugins/webhooks/demo/phdcomics/helper/__init__.py
A config/plugins/webhooks/demo/phdcomics/static/script.js
A config/plugins/webhooks/demo/phdcomics/static/styles.css
A config/plugins/webhooks/demo/trans_object/config/trans_object.yaml
A config/plugins/webhooks/demo/trans_object/helper/__init__.py
A config/plugins/webhooks/demo/xkcd/config/xkcd.yml
A config/plugins/webhooks/demo/xkcd/static/script.js
A config/plugins/webhooks/demo/xkcd/static/styles.css
A doc/source/admin/images_webhooks/history-menu.png
A doc/source/admin/images_webhooks/masthead.png
A doc/source/admin/images_webhooks/masthead_trans_object.png
A doc/source/admin/images_webhooks/tool.png
A doc/source/admin/images_webhooks/workflow.png
A doc/source/admin/webhooks.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webhooks/__init__.py
M static/maps/layout/menu.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
A static/maps/mvc/tool/tool-webhooks.js.map
A static/maps/mvc/webhooks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
A static/scripts/mvc/tool/tool-webhooks.js
A static/scripts/mvc/webhooks.js
A templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev
Commit: 575373c8f304967b224af128774ad646a40cde3b
https://github.com/galaxyproject/galaxy/commit/575373c8f304967b224af128774a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-23 (Sun, 23 Oct 2016)
Changed paths:
R templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
Remove run_complete.mako -- unused and cruft from merge chaos in webhooks PR.
Commit: 65dc4f22aa7b717109aca6fac7947a84d2bd587a
https://github.com/galaxyproject/galaxy/commit/65dc4f22aa7b717109aca6fac794…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-23 (Sun, 23 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
Log Message:
-----------
Merge pull request #3074 from martenson/fix-libraries-prefix
[16.07] Fix libraries prefix
Commit: 20f98df554f502bddff1f22879bf867f97ab7288
https://github.com/galaxyproject/galaxy/commit/20f98df554f502bddff1f22879bf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M lib/galaxy/jobs/runners/cli.py
Log Message:
-----------
Finish job for Torque SSH runner
Commit: 5662a6a5c6fd7166b9f5092308e3ff2ca2bb3738
https://github.com/galaxyproject/galaxy/commit/5662a6a5c6fd7166b9f5092308e3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/metadata.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/__init__.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/topsort.py
M lib/galaxy/web/__init__.py
M lib/galaxy/web/buildapp.py
M lib/galaxy/web/framework/__init__.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/reports/__init__.py
M lib/galaxy/webapps/tool_shed/__init__.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M scripts/db_shell.py
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Merge pull request #3071 from nsoranzo/fix__all__
Change __all__ from list to tuple [2/2]
Commit: 0f0bcb6a088f669a5c1272d238bbe79e29002742
https://github.com/galaxyproject/galaxy/commit/0f0bcb6a088f669a5c1272d238bb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M Makefile
Log Message:
-----------
fix bad merge in #3060
Commit: 61d25720661cb120afc7b44c57f41a1b245e21e4
https://github.com/galaxyproject/galaxy/commit/61d25720661cb120afc7b44c57f4…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M lib/galaxy/jobs/runners/cli.py
Log Message:
-----------
More explcit logging of CLI runner state change (thx @nsoranzo)
Commit: 00c48e4878a0b22ce7045692d67d72af7d540215
https://github.com/galaxyproject/galaxy/commit/00c48e4878a0b22ce7045692d67d…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M Makefile
Log Message:
-----------
remove the rest of the badle merged target
Commit: 05be84ba47c0932a393cb9925ae10db4fae27396
https://github.com/galaxyproject/galaxy/commit/05be84ba47c0932a393cb9925ae1…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M Makefile
Log Message:
-----------
Merge pull request #3087 from martenson/fix-makefile
fix bad merge in #3060
Commit: 4bfac4536971c54a704c76de083de0600332442c
https://github.com/galaxyproject/galaxy/commit/4bfac4536971c54a704c76de083d…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M doc/patch.py
Log Message:
-----------
Fix flake8 errors and Python3 compatibility for doc/patch.py
Commit: a21ed34efb695fb71f1c7616dc1655de8b54be41
https://github.com/galaxyproject/galaxy/commit/a21ed34efb695fb71f1c7616dc16…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
R doc/source/admin/interactive_environments_success.png
A doc/source/dev/interactive_environments_success.png
Log Message:
-----------
Move png in the right directory
Broken in #2543.
Commit: 8a17143bc77ce370974e35f51d699f8029edd647
https://github.com/galaxyproject/galaxy/commit/8a17143bc77ce370974e35f51d69…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
R doc/source/lib/galaxy.util.backports.importlib.rst
R scripts/bootstrap_history_announce_template.rst
Log Message:
-----------
Remove unused files
Commit: e6d0b69ec89786f56fa71d2e893b2361bbe55d0e
https://github.com/galaxyproject/galaxy/commit/e6d0b69ec89786f56fa71d2e893b…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M doc/source/dev/build_a_job_runner.rst
A doc/source/dev/inherit.png
A doc/source/dev/queue.png
A doc/source/dev/queue_b.png
A doc/source/dev/runner_diag.png
Log Message:
-----------
Add and use local images for build runner doc
Commit: 3180b631662ced589fe9db42d27caa58638b5f8d
https://github.com/galaxyproject/galaxy/commit/3180b631662ced589fe9db42d27c…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M .gitignore
M Makefile
M doc/Makefile
M doc/parse_gx_xsd.py
M doc/schema_template.md
M doc/source/dev/index.rst
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Properly integrate tool XML schema with docs
Generate intermediate rst file instead of html
Move generation to doc/Makefile
Use pandoc to generate table of contents and fragment ids.
Remove nested inline markup (not supported by reStructuredText)
Fix https and other links.
Commit: 527e332aa39e82224965e6aaef94ffaa1cf956bf
https://github.com/galaxyproject/galaxy/commit/527e332aa39e82224965e6aaef94…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
M doc/source/admin/interactive_environments.rst
M doc/source/admin/mulled_containers.rst
M doc/source/conf.py
M doc/source/index.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.rst
M doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07.rst
M doc/source/releases/index.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/managers/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/bootstrap_history.py
M scripts/galaxy-main
Log Message:
-----------
Fix a bunch of errors reported by Sphinx
Commit: 10ce532c15a5ab7373f40a1452f3e1ed236d3ec7
https://github.com/galaxyproject/galaxy/commit/10ce532c15a5ab7373f40a1452f3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M test/qunit/package.json
Log Message:
-----------
Fix qunit local testing install -- now runs on modern node (v6.9.1) with no system packages, just 'npm install', 'grunt'.
Commit: ae0d0a23e273d39f64da2550da34adee9a540bb2
https://github.com/galaxyproject/galaxy/commit/ae0d0a23e273d39f64da2550da34…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M doc/source/slideshow/architecture/images/galaxy_schema.png
Log Message:
-----------
Update the schema to be correct and recent
Commit: d2ff7345a8c0fbdb8c5d88e86e428f79c263d462
https://github.com/galaxyproject/galaxy/commit/d2ff7345a8c0fbdb8c5d88e86e42…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
Log Message:
-----------
Remove 4 additional mako files per nsoranzo
Commit: 9d402eaf1ab13b03894a27645368f12a9d42289c
https://github.com/galaxyproject/galaxy/commit/9d402eaf1ab13b03894a27645368…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Merge remote-tracking branch 'tmcgowan/frequest_943' into dev
Commit: 62c77e2cc457a5cb2f33b7d75e247ecf13ba57d8
https://github.com/galaxyproject/galaxy/commit/62c77e2cc457a5cb2f33b7d75e24…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M doc/source/slideshow/architecture/images/galaxy_schema.png
Log Message:
-----------
Merge pull request #3091 from dannon/update_old_schema
Update the schema image in architecture slides to be correct and recent (and use git-lfs for doc pngs)
Commit: 8da4ad6563f2d37309494aa86e1f8ed2595a6af9
https://github.com/galaxyproject/galaxy/commit/8da4ad6563f2d37309494aa86e1f…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
R templates/webapps/galaxy/workflow/run_complete.mako
Log Message:
-----------
Merge pull request #3082 from dannon/remove_run_complete
Remove run_complete.mako -- unused and cruft from merge chaos in webh…
Commit: 17da51abdc61e9fb1e3f76b36316c9dbf3c836e6
https://github.com/galaxyproject/galaxy/commit/17da51abdc61e9fb1e3f76b36316…
Author: Peter Cock <p.j.a.cock(a)googlemail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Include filenames in loc file DEBUG lines
This will help debugging where multiple (possibly conflicting) ``*.loc`` files come from, e.g.
```
galaxy.tools.data DEBUG 2016-10-25 18:34:50,841 Loaded tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2016-10-25 18:34:51,356 Loaded tool data table 'blastdb'
galaxy.tools.data DEBUG 2016-10-25 18:34:51,359 Loading another instance of data table 'blastdb_p', attempting to merge content.
galaxy.tools.data DEBUG 2016-10-25 18:34:51,375 Loaded tool data table 'blastdb_d'
```
Evidently I may have at least two copies of ``blastdb_p.loc``, but where are they?
Commit: f891034390908bd6a374bf140a57ac76afefefd9
https://github.com/galaxyproject/galaxy/commit/f891034390908bd6a374bf140a57…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-10-25 (Tue, 25 Oct 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Lowercase the datatypes, add edam_data, thanks @nsoranzo
Commit: 35346fdb3e6764b14ae3359fb9ea31c03d932ea0
https://github.com/galaxyproject/galaxy/commit/35346fdb3e6764b14ae3359fb9ea…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Merge pull request #3095 from peterjc/patch-4
Include filenames in loc file DEBUG lines
Commit: ca8cd524a1f882b7de2aaf5f56d8b2878c07739a
https://github.com/galaxyproject/galaxy/commit/ca8cd524a1f882b7de2aaf5f56d8…
Author: Peter Cock <p.j.a.cock(a)googlemail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Avoid pointless lambda function
The lambda function used a ternary if/else anyway, just do this directly - its shorter and clearer.
Commit: fc027124e73ee391e4b4045b2abc68fd942f910c
https://github.com/galaxyproject/galaxy/commit/fc027124e73ee391e4b4045b2abc…
Author: Peter Cock <p.j.a.cock(a)googlemail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M config/tool_data_table_conf.xml.sample
Log Message:
-----------
Fix BLAST database *.loc files inconsistency
We should have all of the ``blast*.loc`` files in the sample configuration, or none of them.
Historically Galaxy included only the nucleotide BLAST database ``blastdb.loc`` file for use with mega-blast, with ``blastdb_p.loc`` later for protein databases added as part of the BLAST+ suite (which initially was in the main Galaxy repository).
In a3018feb028658fc3a7071803b7b49cb575e7358 the mega-blast tool was moved to the Tool Shed, and the ``blastdb.loc`` entry removed. Likewise the BLAST+ tools were moved to the Tool Shed, but the ``blastdb_p.loc`` entry remains.
Later (on the Tool Shed only?) ``blastdb_d.loc``was added for protein domain databases.
Commit: ab42b7b15c50c7ae4a4a582ebc1df2780e1538de
https://github.com/galaxyproject/galaxy/commit/ab42b7b15c50c7ae4a4a582ebc1d…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Merge pull request #3097 from peterjc/patch-4
Avoid pointless lambda function
Commit: 90d143cda16d7c7a0938e255c08bf9db7fea727c
https://github.com/galaxyproject/galaxy/commit/90d143cda16d7c7a0938e255c08b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M config/tool_data_table_conf.xml.sample
Log Message:
-----------
Merge pull request #3098 from peterjc/patch-6
Fix BLAST database *.loc files inconsistency
Commit: 2ec9c05380356ba543b29bae44cc3bdd947196a2
https://github.com/galaxyproject/galaxy/commit/2ec9c05380356ba543b29bae44cc…
Author: Peter Cock <p.j.a.cock(a)googlemail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Log loading of resources from *.loc files
Example output:
```
$ grep "lines from" paster.log
galaxy.tools.data DEBUG 2016-10-26 10:24:22,742 Loaded 0 lines from 'tool-data/all_fasta.loc' for 'all_fasta'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,753 Loaded 0 lines from 'tool-data/bfast_indexes.loc' for 'bfast_indexes'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,848 Loaded 24 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,859 Loaded 0 lines from 'tool-data/maf_index.loc' for 'indexed_maf_files'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,865 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc' for 'ngs_sim_fasta'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,878 Loaded 0 lines from 'tool-data/perm_base_index.loc' for 'perm_base_indexes'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,890 Loaded 0 lines from 'tool-data/perm_color_index.loc' for 'perm_color_indexes'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,895 Loaded 0 lines from 'tool-data/picard_index.loc' for 'picard_indexes'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,899 Loaded 0 lines from 'tool-data/picard_index.loc' for 'srma_indexes'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,937 Loaded 0 lines from 'tool-data/mosaik_index.loc' for 'mosaik_indexes'
galaxy.tools.data DEBUG 2016-10-26 10:24:22,943 Loaded 0 lines from 'tool-data/twobit.loc' for 'twobit'
...
galaxy.tools.data DEBUG 2016-10-26 10:24:24,036 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb.loc' for 'blastdb'
galaxy.tools.data DEBUG 2016-10-26 10:24:24,106 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_p.loc' for 'blastdb_p'
galaxy.tools.data DEBUG 2016-10-26 10:24:24,112 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_d.loc' for 'blastdb_d'
```
Commit: f21279d473fa8f19d3881af35d3066e79d757304
https://github.com/galaxyproject/galaxy/commit/f21279d473fa8f19d3881af35d30…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/tools/data/__init__.py
Log Message:
-----------
Merge pull request #3099 from peterjc/patch-5
Log loading of resources from *.loc files
Commit: a6f1783b366293a0d87ee941882e449f092cce95
https://github.com/galaxyproject/galaxy/commit/a6f1783b366293a0d87ee941882e…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
A lib/galaxy/datatypes/test/test.CEL
Log Message:
-----------
Small test case CEL datatype, v4
Commit: 827e61a98cdfb3074d49df25b3ac0b30ce32d0bc
https://github.com/galaxyproject/galaxy/commit/827e61a98cdfb3074d49df25b3ac…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Add doctests
Commit: 5c1d0982e33e3c5464bb6374d33ed9a7bb76a648
https://github.com/galaxyproject/galaxy/commit/5c1d0982e33e3c5464bb6374d33e…
Author: nturaga <nitesh.turaga(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
lint issues
Commit: 541643d7fe28abeac4a69147aa3ae30f84d438ae
https://github.com/galaxyproject/galaxy/commit/541643d7fe28abeac4a69147aa3a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/test/test.CEL
Log Message:
-----------
Merge pull request #3073 from nturaga/add_cel_datatype
Add CEL datatype
Commit: 66dec1d580b426ad955db03608ec7da7eb5c5018
https://github.com/galaxyproject/galaxy/commit/66dec1d580b426ad955db03608ec…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-26 (Wed, 26 Oct 2016)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M test/base/driver_util.py
Log Message:
-----------
Add download_to_file function to galaxy.util
Use it in 2 places:
- test/base/driver_util.py (thus adding timeout and chunking)
- lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
where the total download timeout is substituted with the usual
urllib timeout
Commit: 0eff2ec6479b321d9fc653aa9eaf79559fc50e56
https://github.com/galaxyproject/galaxy/commit/0eff2ec6479b321d9fc653aa9eaf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge remote-tracking branch 'tmcgowan/issue_3000' into dev
Commit: 6e4f3d9d2d1a01b539d412aad5bb8fbe0ba95a17
https://github.com/galaxyproject/galaxy/commit/6e4f3d9d2d1a01b539d412aad5bb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Revert menu.js, tool-form.js to pre-webhooks-PR
Commit: 83a29454caea72915386c58a7188e08cd4597d35
https://github.com/galaxyproject/galaxy/commit/83a29454caea72915386c58a7188…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Lint fixes to workflow controller
Commit: 660d70f8b4da32f5ebd5981ad9eb27e87a79da73
https://github.com/galaxyproject/galaxy/commit/660d70f8b4da32f5ebd5981ad9eb…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #3103 from dannon/minor_style_fixes
Lint fixes to workflow controller
Commit: 62773a72c728b8bab46804d2128e46f62d45cd1d
https://github.com/galaxyproject/galaxy/commit/62773a72c728b8bab46804d2128e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Reapply isolated menu.js webhook changes
Commit: 67b1d45e3657af077005ed7b0b1469a7fd3f42d0
https://github.com/galaxyproject/galaxy/commit/67b1d45e3657af077005ed7b0b14…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Reapply isolated tool-form.js webhook changes
Commit: 2458c5455fe07c7832cb30fd5bdedc9770db6f42
https://github.com/galaxyproject/galaxy/commit/2458c5455fe07c7832cb30fd5bde…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #3102 from dannon/fix_webhook_js_merge
Fixes for remaining webhooks PR issues.
Commit: d9dfc2cc78339f9b2158a07fff3df0a24d081865
https://github.com/galaxyproject/galaxy/commit/d9dfc2cc78339f9b2158a07fff3d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
A static/maps/mvc/ui/ui-thumbnails.js.map
A static/scripts/mvc/ui/ui-thumbnails.js
M static/style/blue/base.css
Log Message:
-----------
Move thumbnail list view to shared ui elements
Commit: 296ef7e232468a2311ba18763752d97e10c63a2d
https://github.com/galaxyproject/galaxy/commit/296ef7e232468a2311ba18763752…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M static/maps/mvc/ui/ui-tabs.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
Log Message:
-----------
Hide tabs navigation if there is only one tab
Commit: aab59be19160a97f41c60b7dab741825c90be934
https://github.com/galaxyproject/galaxy/commit/aab59be19160a97f41c60b7dab74…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix margin
Commit: ec9ca3ffd1bcb2a6e70a5a1f2c8e0183e80ddc1a
https://github.com/galaxyproject/galaxy/commit/ec9ca3ffd1bcb2a6e70a5a1f2c8e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M config/plugins/visualizations/charts/static/client/views/editor.js
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/mvc/ui/ui-thumbnails.js
Log Message:
-----------
Fix list view title
Commit: 0b1c171ebc2b9b0605a6ef1e8e5b68e20d579c74
https://github.com/galaxyproject/galaxy/commit/0b1c171ebc2b9b0605a6ef1e8e5b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M config/plugins/visualizations/charts/static/client/views/editor.js
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Revise tab viewer, add test cases
Commit: c4526bdaba29ccc9b045dea429dbc0c3fa0e5b15
https://github.com/galaxyproject/galaxy/commit/c4526bdaba29ccc9b045dea429db…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M static/maps/mvc/ui/ui-tabs.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
Log Message:
-----------
Hide tab navbar if there is only one tab available
Commit: 05fbef510c7497911a2abea83c5bdc26bf338460
https://github.com/galaxyproject/galaxy/commit/05fbef510c7497911a2abea83c5b…
Author: Anthony Bretaudeau <abretaud(a)irisa.fr>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Add doc for conda_copy_dependencies option
Discussed on IUC gitter, related to https://github.com/galaxyproject/galaxy/issues/3008
Commit: 16866b5e8075d648bd17ac3786f76356e23c43a2
https://github.com/galaxyproject/galaxy/commit/16866b5e8075d648bd17ac3786f7…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
add extra time problem
Commit: 69cda7ee10d78a61830f90f957500ba41821640b
https://github.com/galaxyproject/galaxy/commit/69cda7ee10d78a61830f90f95750…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
clarify links
Commit: 19b568cb9310b03b0cc74d3e6a7745b83074a0b8
https://github.com/galaxyproject/galaxy/commit/19b568cb9310b03b0cc74d3e6a77…
Author: Greg Von Kuster <ghv2(a)psu.edu>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Fix XSD for exclude_min and exclude_max attributes of tool param validator
Commit: 838e2cbb66f2d7138eed51e434e623f057625042
https://github.com/galaxyproject/galaxy/commit/838e2cbb66f2d7138eed51e434e6…
Author: Jim Johnson <jj(a)umn.edu>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add routes to get genomes indexes and sequences
So igv.js can retrieve genome data
Commit: ac9d21d510320de98d7db87fd97e1246d468728a
https://github.com/galaxyproject/galaxy/commit/ac9d21d510320de98d7db87fd97e…
Author: James Taylor <james(a)jamestaylor.org>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Eagerload tags and annotations in history display
Commit: c626ff8b2effa390de4816eafe507ea5b1fd1d6b
https://github.com/galaxyproject/galaxy/commit/c626ff8b2effa390de4816eafe50…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-28 (Fri, 28 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Merge pull request #3110 from jxtx/dev
Eagerload tags and annotations in history display
Commit: a1e5118050ee5cf827396e2b2b38f147c51ed772
https://github.com/galaxyproject/galaxy/commit/a1e5118050ee5cf827396e2b2b38…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #3109 from jj-umn/patch-5
Add routes to get genomes indexes and sequences
Commit: 29b07cbb2a5aa05eb3636dcd9c3f0e15c42d21a1
https://github.com/galaxyproject/galaxy/commit/29b07cbb2a5aa05eb3636dcd9c3f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3108 from gregvonkuster/xsd
Fix XSD for exclude_min and exclude_max
Commit: f0c5d5ca39d1e7456aea0d81fdcba345ce28a868
https://github.com/galaxyproject/galaxy/commit/f0c5d5ca39d1e7456aea0d81fdcb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M test/qunit/package.json
Log Message:
-----------
Merge pull request #3089 from dannon/fix_local_qunit
Fix qunit local testing install -- now runs on modern node (v6.9.1) w…
Commit: f9ee0f86376f90ede636e4874cca120d30e7cd8c
https://github.com/galaxyproject/galaxy/commit/f9ee0f86376f90ede636e4874cca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M Makefile
M doc/Makefile
M doc/parse_gx_xsd.py
M doc/patch.py
M doc/schema_template.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments_success.png
M doc/source/admin/mulled_containers.rst
M doc/source/conf.py
M doc/source/dev/build_a_job_runner.rst
M doc/source/dev/index.rst
A doc/source/dev/inherit.png
A doc/source/dev/interactive_environments_success.png
A doc/source/dev/queue.png
A doc/source/dev/queue_b.png
A doc/source/dev/runner_diag.png
M doc/source/index.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
R doc/source/lib/galaxy.util.backports.importlib.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.rst
M doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07.rst
M doc/source/releases/index.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/managers/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/simplegraph.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/bootstrap_history.py
R scripts/bootstrap_history_announce_template.rst
M scripts/galaxy-main
Log Message:
-----------
Merge pull request #3086 from nsoranzo/fix_doc
Properly integrate tool XML schema with docs
Commit: 25527bec32b2431f1a8769ef79f34ad9af38c0db
https://github.com/galaxyproject/galaxy/commit/25527bec32b2431f1a8769ef79f3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
M static/maps/mvc/ui/ui-tabs.js.map
A static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
M static/style/blue/base.css
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge pull request #3079 from guerler/reusable_grid_view
Move thumbnail list view to shared ui elements, revise tabs, add test cases
Commit: 9e1331f1b37a40d8894fc724bb745589bc5e213b
https://github.com/galaxyproject/galaxy/commit/9e1331f1b37a40d8894fc724bb74…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
Log Message:
-----------
Merge pull request #3049 from lparsons/bam_to_bigwig
Sort bedtools output in bam_to_bigwig conversion
Commit: aaf5b4d0f8a823d9b3d659b55f25ce207c47e25e
https://github.com/galaxyproject/galaxy/commit/aaf5b4d0f8a823d9b3d659b55f25…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Merge pull request #3080 from tmcgowan/frequest_1842
Extend PUT /api/workflows/{id} with additional workflow properties
Commit: 6082f790438d6fc04f313c2eef273bfa43ff0715
https://github.com/galaxyproject/galaxy/commit/6082f790438d6fc04f313c2eef27…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-01 (Tue, 01 Nov 2016)
Changed paths:
M run_tool_shed.sh
Log Message:
-----------
Fix path
Broken in #2131.
Reported by @dnbenso at
https://github.com/galaxyproject/galaxy/commit/f2bd242a2c28954215fb84d289d1…
Commit: ce1c7e41c6d90e1ca7d00c68afbd4fca8f55115e
https://github.com/galaxyproject/galaxy/commit/ce1c7e41c6d90e1ca7d00c68afbd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-01 (Tue, 01 Nov 2016)
Changed paths:
M doc/Makefile
Log Message:
-----------
Restore XML formatting for schema document.
Commit: 38dd9ca509ed50b3cf48689522ee884226cc1219
https://github.com/galaxyproject/galaxy/commit/38dd9ca509ed50b3cf48689522ee…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-11-01 (Tue, 01 Nov 2016)
Changed paths:
M doc/Makefile
Log Message:
-----------
Merge pull request #3113 from jmchilton/schema_build
Restore XML formatting for tool schema document.
Commit: 9abe863f26ba742c9f362b3a8177af5c8efa5741
https://github.com/galaxyproject/galaxy/commit/9abe863f26ba742c9f362b3a8177…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-01 (Tue, 01 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix loading of collection operations
If MODEL_TOOLS_PATH is not absolute, it will be joined with tool_path
(i.e. './tools' ) inside _load_tool_tag_set(), so Galaxy will try to load
e.g. './tools/lib/galaxy/tools/unzip_collection.xml'
Commit: 5963a2fa22e64b5494a1aa00931808a11d792cbd
https://github.com/galaxyproject/galaxy/commit/5963a2fa22e64b5494a1aa009318…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #3115 from nsoranzo/release_16.07_fix_collection_ops_loading
[16.07] Fix loading of collection operations
Commit: ef3e63e6d7327719a4581bb939dff8fd1ac1fcd9
https://github.com/galaxyproject/galaxy/commit/ef3e63e6d7327719a4581bb939df…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M templates/user/index.mako
Log Message:
-----------
Merge branch 'release_16.07' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
Commit: 892237bf0042e458db7c7220eb4faf022b5a7650
https://github.com/galaxyproject/galaxy/commit/892237bf0042e458db7c7220eb4f…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix linting broken in #3080
Also fix import order and Python3 compatibility.
Commit: aa72f4a0b62a7795bc726dd75bdb7635d29afef5
https://github.com/galaxyproject/galaxy/commit/aa72f4a0b62a7795bc726dd75bdb…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Merge pull request #3116 from nsoranzo/fix_for_3080
Fix linting broken in #3080
Commit: e06581c587cdfe24822fba2f79ddaf60619858d2
https://github.com/galaxyproject/galaxy/commit/e06581c587cdfe24822fba2f79dd…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Extended the linter rules to accept a help attribute for sections
Commit: 8f89a04eae27e615434e268f93d492b6c0cd54be
https://github.com/galaxyproject/galaxy/commit/8f89a04eae27e615434e268f93d4…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Fix job_working_directory commented default
Follow-up to commit 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726.
Commit: 83760e6a01cd3fa16a17158bb1182ffebb00c5d7
https://github.com/galaxyproject/galaxy/commit/83760e6a01cd3fa16a17158bb118…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M doc/source/conf.py
Log Message:
-----------
Don't skip __init__() methods when generating docs
Commit: 402f2815c23d695f0673d0af9acb9cf0e3527afa
https://github.com/galaxyproject/galaxy/commit/402f2815c23d695f0673d0af9acb…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Drop code which is never executed
After commit 59583f26ea11b44cb17f260230be820b304cd918,
self.object_store_config_file is always set.
Commit: ad515397388056b8587c80350b755444602a49d0
https://github.com/galaxyproject/galaxy/commit/ad515397388056b8587c80350b75…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/jobs/command_factory.py
Log Message:
-----------
Fix typo
Commit: 0c28a64269048ea21701e6c5b358d783bdde8eed
https://github.com/galaxyproject/galaxy/commit/0c28a64269048ea21701e6c5b358…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/objectstore/rods.py
Log Message:
-----------
Remove redundant ObjectStore superclass
Commit: 1c68e0af3e9a02250d0d12c2149dcdbb1caf2da2
https://github.com/galaxyproject/galaxy/commit/1c68e0af3e9a02250d0d12c2149d…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-02 (Wed, 02 Nov 2016)
Changed paths:
M lib/galaxy/objectstore/__init__.py
Log Message:
-----------
Fix object stores' __init__() methods doc
Also:
- remove unused parameters when calling the parent constructors
- Python3 compatibility
Commit: 94fd3a51a2a3a46aa4a834ed6d7d0bb50e6154a5
https://github.com/galaxyproject/galaxy/commit/94fd3a51a2a3a46aa4a834ed6d7d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M doc/source/conf.py
M lib/galaxy/config.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/rods.py
Log Message:
-----------
Merge pull request #3119 from nsoranzo/misc_fixes
Object store and other misc fixes
Commit: 65338b3adb925f27142c6fdf45af7f8d01e57f9d
https://github.com/galaxyproject/galaxy/commit/65338b3adb925f27142c6fdf45af…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M run_tool_shed.sh
Log Message:
-----------
Merge pull request #3112 from nsoranzo/release_16.04_fix_for_2131
[16.04] Fix path in run_tool_shed.sh
Commit: d72cc77bebd46b0e60d09e19cee2496777503f11
https://github.com/galaxyproject/galaxy/commit/d72cc77bebd46b0e60d09e19cee2…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M run_tool_shed.sh
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Commit: 1d8f31c4f488dc380ffe657e5fa4a9d9cdd697ae
https://github.com/galaxyproject/galaxy/commit/1d8f31c4f488dc380ffe657e5fa4…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M run_tool_shed.sh
Log Message:
-----------
Merge branch 'release_16.07' into dev
Commit: d3a5c4c7205b269830547fcb647528e3e2a9663f
https://github.com/galaxyproject/galaxy/commit/d3a5c4c7205b269830547fcb6475…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Catch and display exceptions triggered by tool filter functions
Commit: 300c9616306f69579b1d492aa78a17985e21f738
https://github.com/galaxyproject/galaxy/commit/300c9616306f69579b1d492aa78a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-03 (Thu, 03 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Use as instead of comma
Commit: 5e19d6c57465ce79d4ee96e3206542ac655d137d
https://github.com/galaxyproject/galaxy/commit/5e19d6c57465ce79d4ee96e32065…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Escape section id and name when writing integrated_tool_panel.xml
This should fix #3084.
Commit: 4866e72ad22b1772f93c8973e51f32086896277f
https://github.com/galaxyproject/galaxy/commit/4866e72ad22b1772f93c8973e51f…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Merge pull request #3122 from mvdbeek/escape_sections
Escape section name when writing to xml,
Commit: d5132a374c25d17e63a19379bcec1d42b99f8547
https://github.com/galaxyproject/galaxy/commit/d5132a374c25d17e63a19379bcec…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Log invalid xml filename
Commit: 51c586c264f2acd912060297804d61c2539f2483
https://github.com/galaxyproject/galaxy/commit/51c586c264f2acd912060297804d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix tools placed outside of panel section
Occasionally tools were being installed outside of the selected too panel
section. In the log one would find contradicting messages such as
```
tool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'.
galaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools
172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] "POST
/admin_toolshed/prepare_for_install HTTP/1.1" 200 -
"http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e…"
"
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/54.0.2840.71 Safari/537.36
nvalid tool_panel_section_key "ncbi_sra_tools" specified. Tools will be
loaded outside of sections in the tool panel.
```
The intermittent POST is picked up by a different thread, that didn't
have its toolbox updated with the new section.
To circumvent this, we send the `create_panel_section` task to all
threads.
Commit: 4365b907293e366d4ad48396bb5c9dc00f134611
https://github.com/galaxyproject/galaxy/commit/4365b907293e366d4ad48396bb5c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Fix toolbox unittests
Commit: a3ac57dbc532320c98e0b4a72772663293ab3b06
https://github.com/galaxyproject/galaxy/commit/a3ac57dbc532320c98e0b4a72772…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Remove verbose_install_check option
This option was introduced with #2554 and #2538, in reponse to a false
positive conda install. This would have been caught by simply checking
the exit code, which we are doing by default now. The additional
verification is too strigent and not in line with the conda resolver.
Activating this option will report perfectly well installed conda
environments as having failed and will cause them to be uninstalled.
Commit: 37399049552dd1f2f4492e4eb9f168ac8a9abd5f
https://github.com/galaxyproject/galaxy/commit/37399049552dd1f2f4492e4eb9f1…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge pull request #3124 from mvdbeek/escape_sections
Log invalid xml filename
Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6
https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Escape section id and name when writing integrated_tool_panel.xml
This should fix #3084.
Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9
https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Log invalid xml filename
Commit: 2956f94aa06f62fc0adde93d5aacc69e693a62d8
https://github.com/galaxyproject/galaxy/commit/2956f94aa06f62fc0adde93d5aac…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
Log Message:
-----------
BLAST database *.loc.sample files
Commit: 2e36fdb0bd0fff246eeff6322542c31150804eb2
https://github.com/galaxyproject/galaxy/commit/2e36fdb0bd0fff246eeff6322542…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M config/tool_data_table_conf.xml.sample
Log Message:
-----------
Include all three BLAST .loc files in data table conf
Commit: f060795335e564f79ed3f28b5390db4ac8e7d735
https://github.com/galaxyproject/galaxy/commit/f060795335e564f79ed3f28b5390…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
A lib/galaxy/datatypes/blast.py
Log Message:
-----------
BLAST datatypes as of standalone blast_datatypes v0.0.21
Copied from separate BLAST+ Galaxy repository,
https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatyp…
Currently available from the Galaxy Tool Shed,
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Primary contributors to the BLAST datatypes for Galaxy:
* Peter Cock (The James Hutton Institute, UK)
* Edward Kirton
* Nicola Soranzo
* Bjoern Gruening
This work and the associated BLAST+ wrappers can be cited as:
NCBI BLAST+ integrated into Galaxy.
P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
*GigaScience* 2015, 4:39
DOI: http://dx.doi.org/10.1186/s13742-015-0080-7
Commit: a53e9fa9dbd635ee6359fb6b68371a3d0e5159c6
https://github.com/galaxyproject/galaxy/commit/a53e9fa9dbd635ee6359fb6b6837…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Remove unused imports
Commit: bdd046a2e86c935e1c932421a25e7ed480aacdf8
https://github.com/galaxyproject/galaxy/commit/bdd046a2e86c935e1c932421a25e…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Missing import required for use as doctest
Commit: 193651c88d325a5c1710def37386524e956ac147
https://github.com/galaxyproject/galaxy/commit/193651c88d325a5c1710def37386…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
Log Message:
-----------
Sample blastxml file for sniff doctest
Commit: ea717dd0013c9ef69d5ea0cd8edb72f44546e5d8
https://github.com/galaxyproject/galaxy/commit/ea717dd0013c9ef69d5ea0cd8edb…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Add BLAST datatypes to datatypes_conf.xml.sample
Commit: 8b73de6f50572ea2fb815fa75460f5850b877f12
https://github.com/galaxyproject/galaxy/commit/8b73de6f50572ea2fb815fa75460…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Adjust import order as per Galaxy tox flake8 checks
Commit: f9eff95613cdf27f5300ea393418f017da8e8012
https://github.com/galaxyproject/galaxy/commit/f9eff95613cdf27f5300ea393418…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
More accurate module docstring
Commit: 0152254a6f455bae538c96f3ce85baee1ae1c9f8
https://github.com/galaxyproject/galaxy/commit/0152254a6f455bae538c96f3ce85…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
megablast_xml_parser_test1.blastxml should now sniff as blastxml
Commit: 48664fa2fe7f43ee667e9fa4ece51852632570e7
https://github.com/galaxyproject/galaxy/commit/48664fa2fe7f43ee667e9fa4ece5…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Ensure all BLAST datatype contributors in CONTRIBUTORS.md
Commit: ce5ceeb29b134a84cf577f0bf2244011ac0cdfe4
https://github.com/galaxyproject/galaxy/commit/ce5ceeb29b134a84cf577f0bf224…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M CONTRIBUTORS.md
Log Message:
-----------
Give my work email address as well.
My Galaxy work to date has been while employed at
The James Hutton Institute (UK).
Commit: 17783cec36f4bf0d3b79137842dad52a64f80da2
https://github.com/galaxyproject/galaxy/commit/17783cec36f4bf0d3b79137842da…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
Log Message:
-----------
Tweak testing installing BLAST datatypes from Tool Shed
This is a short term pragmatic solution for the planned return
of the BLAST datatypes to the main Galaxy distribution. Long
term an additional test using an alternative Tool Shed defined
datatype may be needed.
Commit: 7fe47735209e43501e6116453a2fd961e5934429
https://github.com/galaxyproject/galaxy/commit/7fe47735209e43501e6116453a2f…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Clearer error message if BLAST XML header too long
Commit: 4159770ed9d173a2a3b45f7615aa764be9e99188
https://github.com/galaxyproject/galaxy/commit/4159770ed9d173a2a3b45f7615aa…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Explicitly label blast.py as MIT licensed.
Edward Kirton's contributions were made under the MIT license
while this code was developed outside of the main Galaxy
Project and distributed via the Galaxy Tool Shed). We have not
been able to contact him to authorise re-licensing under the
main Galaxy Project's license instead.
Commit: b5ba9605e56b8a8c8a827c6bd83208314ab8ccf0
https://github.com/galaxyproject/galaxy/commit/b5ba9605e56b8a8c8a827c6bd832…
Author: peterjc <p.j.a.cock(a)googlemail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/blast.py
Log Message:
-----------
Mark BLAST XML with EDAM ontology terms.
As per Herve Menager, EDAM format should be 3331 and data 0857
(sequence search results).
Commit: b1892b7e30f9e2a9be94bd8ee064c0f548525bfe
https://github.com/galaxyproject/galaxy/commit/b1892b7e30f9e2a9be94bd8ee064…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/util/__init__.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M test/base/driver_util.py
Log Message:
-----------
Merge pull request #3100 from nsoranzo/followup_on_3013
Add download_to_file function to galaxy.util
Commit: 1c740833e0c1884d43a42dc4417eb3f02adfafab
https://github.com/galaxyproject/galaxy/commit/1c740833e0c1884d43a42dc4417e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix import order
Commit: c5245219567562f67556548cbc0b8a9624ea0308
https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/util/__init__.py
Log Message:
-----------
Make catching XML parsing errors python2.6 compatible
Commit: 7456b1f9218dabd6eab0d2fa6c3acc285c6c20c3
https://github.com/galaxyproject/galaxy/commit/7456b1f9218dabd6eab0d2fa6c3a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Remove unnecessary slashes
Commit: 4d623a4d5a391a6aed2faf4b45f03c87b8f11a90
https://github.com/galaxyproject/galaxy/commit/4d623a4d5a391a6aed2faf4b45f0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-04 (Fri, 04 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Ensure that label key exists before attempting removal
Commit: 58b7b6cf15c57a9a42340baeb2131e42cc76d02d
https://github.com/galaxyproject/galaxy/commit/58b7b6cf15c57a9a42340baeb213…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-05 (Sat, 05 Nov 2016)
Changed paths:
M CONTRIBUTORS.md
M config/datatypes_conf.xml.sample
M config/tool_data_table_conf.xml.sample
A lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
Log Message:
-----------
Merge pull request #2696 from peterjc/blast_datatypes
Returning Blast datatypes to Galaxy core (work-in-progress)
Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1
https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-05 (Sat, 05 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge pull request #3128 from mvdbeek/backport_3122_3124
[16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml
Commit: 202f96c73114fe9f05ed295505243ba17716b0e2
https://github.com/galaxyproject/galaxy/commit/202f96c73114fe9f05ed29550524…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-06 (Sun, 06 Nov 2016)
Changed paths:
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #3125 from mvdbeek/fix_invalid_section_key
Fix tools placed outside of panel section
Commit: 51050653b44c24328d9225b69d9b1b6971b0354c
https://github.com/galaxyproject/galaxy/commit/51050653b44c24328d9225b69d9b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-06 (Sun, 06 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Rework dependency shell command handling
The approach is to always log a warning with stdout and stderr when
the exit code is not 0.
With this change, one can expect logs like the follwing:
```
galaxy.tools.deps.conda_util DEBUG 2016-11-05 15:14:17,373 Executing command: /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie(a)0.12.7 bowtie=0.12.7
127.0.0.1 - - [05/nov./2016:15:14:19 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36"
127.0.0.1 - - [05/nov./2016:15:14:22 +0200] "POST /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - "http://127.0.0.1:8080/admin_toolshed/prepare_for_install" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.90 Safari/537.36"
galaxy.tools.deps.conda_util WARNING 2016-11-05 15:14:24,029 Failed to execute command-line /home/mvandenb/miniconda3/bin/conda create -y --name __bowtie(a)0.12.7 bowtie=0.12.7, stderr was:
-------->>begin stderr<<--------
PackageNotFoundError: Package not found: '' Package missing in current linux-64 channels:
- bowtie 0.12.7*
You can search for packages on anaconda.org with
anaconda search -t conda bowtie
You may need to install the anaconda-client command line client with
conda install anaconda-client
-------->>end stderr<<--------
-------->>begin stdout<<--------
Fetching package metadata ...............
Solving package specifications: .
-------->>end stdout<<--------
galaxy.tools.deps.resolvers.conda DEBUG 2016-11-05 15:14:24,030 Removing failed conda install of bowtie, version '0.12.7'
```
This should be helpful for the more obscure errors that can occur with conda.
Commit: 8a972cc325fd39b71d89f28d9eec62630d9859ac
https://github.com/galaxyproject/galaxy/commit/8a972cc325fd39b71d89f28d9eec…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
be stronger
Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63
https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Conflicts:
lib/galaxy/util/__init__.py
Commit: 53a66c9d46780a4910a8a03de565eb3fb53f5bdc
https://github.com/galaxyproject/galaxy/commit/53a66c9d46780a4910a8a03de565…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/util/__init__.py
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Commit: 3200fa343b12b2c40ad6b3e29b77c6628d66b7a0
https://github.com/galaxyproject/galaxy/commit/3200fa343b12b2c40ad6b3e29b77…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Log Message:
-----------
Merge branch 'release_16.07' into dev
Conflicts:
lib/galaxy/util/__init__.py
Commit: fb69afae28c434f35860ccaa4591e95fe3acfe91
https://github.com/galaxyproject/galaxy/commit/fb69afae28c434f35860ccaa4591…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Update ToolPanelElements instance locally
in addition to Galaxy's IPC call via send_control_task.
Commit: b169299b5efbd144d5ab43f28e079a3fa5cf45a8
https://github.com/galaxyproject/galaxy/commit/b169299b5efbd144d5ab43f28e07…
Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Extended linter rule for help attribute in section
Commit: 192f66a714f3c7dd320550def43d7cd283dfa6af
https://github.com/galaxyproject/galaxy/commit/192f66a714f3c7dd320550def43d…
Author: Gildas Le Corguillé <lecorguille(a)users.noreply.github.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Update galaxy.xsd
Add `hidden_data` in `ParamType`
The context [cufflinks](https://github.com/galaxyproject/tools-devteam/blob/master/tool_…
`planemo lint .`
```
Applying linter tool_xsd... FAIL
.. ERROR: Invalid tmpw5U2MV found. Errors [/tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_ENUMERATION_VALID: Element 'param', attribute 'type': [facet 'enumeration'] The value 'hidden_data' is not an element of the set {'text', 'integer', 'float', 'color', 'boolean', 'genomebuild', 'library_data', 'select', 'data_column', 'hidden', 'baseurl', 'file', 'data', 'drill_down', 'data_collection'}.
/tmp/tmpw5U2MV:144:0:ERROR:SCHEMASV:SCHEMAV_CVC_DATATYPE_VALID_1_2_1: Element 'param', attribute 'type': 'hidden_data' is not a valid value of the atomic type 'ParamType'.
```
I don’t know so much this tag `hidden_data`, but it seems that it’s still in the [Galaxy doc](https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-p…
Commit: 04935ce94b864a7898dc62895a11023dec805580
https://github.com/galaxyproject/galaxy/commit/04935ce94b864a7898dc62895a11…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Merge pull request #3105 from abretaud/patch-2
Add doc for conda_copy_dependencies option
Commit: 78dfb95f0264e349ee03b5c1a7c1cde9c6e38ba4
https://github.com/galaxyproject/galaxy/commit/78dfb95f0264e349ee03b5c1a7c1…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3131 from joachimwolff/dev
Extended the linter rules to accept a help attribute for sections
Commit: 7c030ebf2f51c6800966a2fc2d1b0048f0930f1d
https://github.com/galaxyproject/galaxy/commit/7c030ebf2f51c6800966a2fc2d1b…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M doc/Makefile
Log Message:
-----------
Use sed instead of pandoc to insert TOC in schema doc
pandoc < 1.14 adds the TOC depth as a float, which is not recognised by
Sphinx.
Also, move the TOC after the introduction, which looks nicer.
Commit: 3b8f543ebdd1307c91c3ae719bbb7072476d7b9a
https://github.com/galaxyproject/galaxy/commit/3b8f543ebdd1307c91c3ae719bbb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3132 from lecorguille/patch-2
Update galaxy.xsd
Commit: 6a8ca92dd70bc88bee962cd079460118f998c351
https://github.com/galaxyproject/galaxy/commit/6a8ca92dd70bc88bee962cd07946…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-07 (Mon, 07 Nov 2016)
Changed paths:
M doc/Makefile
Log Message:
-----------
Merge pull request #3135 from nsoranzo/followup_on_3086
Use sed instead of pandoc to insert TOC in schema doc
Commit: 0ba54e922046733e582b7c5b4066525edc3957aa
https://github.com/galaxyproject/galaxy/commit/0ba54e922046733e582b7c5b4066…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Treat the value of `message_box_visible` in galaxy.ini as a boolean
Commit: 7bee2651aa8f08ea0495d167e33d317a22ae3ef9
https://github.com/galaxyproject/galaxy/commit/7bee2651aa8f08ea0495d167e33d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
string_as_bool for message_box_visible on webapps
Commit: 1e142dd33d505436e081306bc08f044bb7b5886a
https://github.com/galaxyproject/galaxy/commit/1e142dd33d505436e081306bc08f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
User activation emails are sent without a From: address if email_from is
unset. Fix this by using `galaxy-no-reply@host` as with other emails we
send.
Commit: 3d69a2d1a5f7ee5606834c45e34e341fa4822721
https://github.com/galaxyproject/galaxy/commit/3d69a2d1a5f7ee5606834c45e34e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Merge pull request #3139 from natefoo/message-box-bool
Treat the value of `message_box_visible` in galaxy.ini as a boolean
Commit: 00edc474274a671c1ba4d7e2a64335e0abb614c5
https://github.com/galaxyproject/galaxy/commit/00edc474274a671c1ba4d7e2a643…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-11-08 (Tue, 08 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Merge pull request #3140 from natefoo/activation-from
Ensure a From: address is set for user activation emails
Commit: 7f630ea2ddb279ce963070d87573bac4c66d5027
https://github.com/galaxyproject/galaxy/commit/7f630ea2ddb279ce963070d87573…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-09 (Wed, 09 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/webapps/reports/config.py
Log Message:
-----------
Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9
Also fix import order and Python3 compatibility.
Commit: 93a09d2eb033d8bc8b98a7ca94e80bbb1a80fe60
https://github.com/galaxyproject/galaxy/commit/93a09d2eb033d8bc8b98a7ca94e8…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-11-09 (Wed, 09 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M lib/galaxy/webapps/reports/config.py
Log Message:
-----------
Merge pull request #3141 from nsoranzo/followup_on_3139
Fix flake8 linting broken in 7bee2651aa8f08ea0495d167e33d317a22ae3ef9
Commit: 4b2e875802dcdc0015fb1c05d669e31eb60f01ab
https://github.com/galaxyproject/galaxy/commit/4b2e875802dcdc0015fb1c05d669…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-09 (Wed, 09 Nov 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #3123 from guerler/fix_tool_filters
Display an error message when toolbox filters fails
Commit: 019f554e4e8425635c4ba36d7d2500d3a3a7502c
https://github.com/galaxyproject/galaxy/commit/019f554e4e8425635c4ba36d7d25…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Copy hid attribute to converted datasets for hdas only
Commit: 9c37c6df896312de5d07f93d2c6e1bdcaeff3e53
https://github.com/galaxyproject/galaxy/commit/9c37c6df896312de5d07f93d2c6e…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/tool_shed/tools/tool_validator.py
M scripts/api/filter_failed_datasets_from_collection.py
Log Message:
-----------
Fixes for flake8-import-order 0.11
Also fix Python3 compatibility.
Commit: 2d8cf6b3376b41a6dd9a9ff3f4a82aaae1baa209
https://github.com/galaxyproject/galaxy/commit/2d8cf6b3376b41a6dd9a9ff3f4a8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/tool_shed/tools/tool_validator.py
M scripts/api/filter_failed_datasets_from_collection.py
Log Message:
-----------
Merge pull request #3154 from nsoranzo/fixes_for_new_flake8_import_order
Fixes for flake8-import-order 0.11
Commit: d144f18e7a6eaa5276b2d63f51457eda1befd679
https://github.com/galaxyproject/galaxy/commit/d144f18e7a6eaa5276b2d63f5145…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M doc/source/admin/interactive_environments.rst
Log Message:
-----------
Fix typo in GIE nginx proxy docs
Commit: b748ad1565a1e5064f6e08640c19b09a41b4b2bc
https://github.com/galaxyproject/galaxy/commit/b748ad1565a1e5064f6e08640c19…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M doc/source/admin/interactive_environments.rst
Log Message:
-----------
Merge pull request #3157 from galaxyproject/gie-doc-fix
[16.07] Fix typo in GIE nginx proxy docs
Commit: 3ec7be27952b57cf7e0ad87fdf067cacc5e66856
https://github.com/galaxyproject/galaxy/commit/3ec7be27952b57cf7e0ad87fdf06…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge pull request #3149 from guerler/fix_hid
Explicitly specify attributes which should be copied to converted datasets
Commit: d3f7510b2db932228c76402062bad9095549f5f0
https://github.com/galaxyproject/galaxy/commit/d3f7510b2db932228c76402062ba…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/datatypes/data.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Remove unnecessary set_output_history parameter
Also fix import order and Python3 compatibility.
Commit: 133fd3adfc76216d8808ed7200e7278bdaf87488
https://github.com/galaxyproject/galaxy/commit/133fd3adfc76216d8808ed7200e7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-12 (Sat, 12 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
Log Message:
-----------
Quote all paths in converter tools
Commit: 89e6f77feb4404ecb9e0ba025b5d2168e627ed71
https://github.com/galaxyproject/galaxy/commit/89e6f77feb4404ecb9e0ba025b5d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-12 (Sat, 12 Nov 2016)
Changed paths:
M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
Log Message:
-----------
Don't quote
Commit: 46bd40bdc4c0dbad20084937e1e3ac606def9a3a
https://github.com/galaxyproject/galaxy/commit/46bd40bdc4c0dbad20084937e1e3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-13 (Sun, 13 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
Log Message:
-----------
Merge pull request #3165 from mvdbeek/quote_data_converters
Quote all paths in converter tool xml
Commit: 7955077e635f09b4a0c3fda621406686affe0c0f
https://github.com/galaxyproject/galaxy/commit/7955077e635f09b4a0c3fda62140…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-13 (Sun, 13 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M lib/galaxy/datatypes/data.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Merge pull request #3155 from nsoranzo/remove_set_output_history
Remove unnecessary set_output_history parameter
Commit: bfabe00ea8f07782f0af307b124da8090f2906f2
https://github.com/galaxyproject/galaxy/commit/bfabe00ea8f07782f0af307b124d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-13 (Sun, 13 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #3129 from mvdbeek/conda_error_reporting
Pass dependency shell command errors to log
Commit: ae3bdf31dc815dfce305316fe67776bc6802ec1a
https://github.com/galaxyproject/galaxy/commit/ae3bdf31dc815dfce305316fe677…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-13 (Sun, 13 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #3127 from mvdbeek/remove_verbose_install_check_16.07
[16.07] Remove verbose_install_check option
Commit: 6c4d430d75781dac112f0c7b56fe61208d081f1c
https://github.com/galaxyproject/galaxy/commit/6c4d430d75781dac112f0c7b56fe…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M Makefile
Log Message:
-----------
Add note about building docs to Makefile.
Commit: 727270261750fc71979e7ba9fec96b10091ff104
https://github.com/galaxyproject/galaxy/commit/727270261750fc71979e7ba9fec9…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M lib/galaxy/jobs/runners/cli.py
Log Message:
-----------
Merge pull request #3085 from mvdbeek/fix_torque_ssh
[16.07] Finish job for Torque SSH/CLI runner
Commit: ca4e8914ecddbba007c1f65ff17f51e719c0c149
https://github.com/galaxyproject/galaxy/commit/ca4e8914ecddbba007c1f65ff17f…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/interactive_environments.rst
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge branch 'release_16.07' into dev
Conflicts:
lib/galaxy/tools/deps/conda_util.py
Commit: 66cc4c3bbe4a90cd68d935574691c31b8053804e
https://github.com/galaxyproject/galaxy/commit/66cc4c3bbe4a90cd68d935574691…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M Makefile
Log Message:
-----------
Merge pull request #3167 from jmchilton/doc_note
Add note about building docs to Makefile.
Commit: 00b147a6649b8fd1112fa76c573fa78db8e58621
https://github.com/galaxyproject/galaxy/commit/00b147a6649b8fd1112fa76c573f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
Log Message:
-----------
Bring in updates from galaxy-lib.
Commit: 7e988bbe097f4f4e3d1f7c5dc3d149ee0c201bd8
https://github.com/galaxyproject/galaxy/commit/7e988bbe097f4f4e3d1f7c5dc3d1…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
Log Message:
-----------
Merge pull request #3169 from jmchilton/galaxy-lib-update-3
Bring in updates from galaxy-lib.
Commit: 3f4033c05d1f2f1437d42da21e5d26e8e3b46ced
https://github.com/galaxyproject/galaxy/commit/3f4033c05d1f2f1437d42da21e5d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Merge remote-tracking branch 'tmcgowan/issue_2100' into dev
Commit: 1d17a29c7947993ae7cca998eff25c1ff998ebdb
https://github.com/galaxyproject/galaxy/commit/1d17a29c7947993ae7cca998eff2…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/style/source_material/circle.py
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/parse_gx_xsd.py
M doc/patch.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/util/workflow_util.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/auth/pam_auth_helper.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/slideshow/build_slideshow.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M test/api/test_workflows.py
M test/api/workflows_format_2/main.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/workflows/test_modules.py
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Fixes for pycodestyle 2.2.0
Commit: 594e44b4fbca2a1d128f81c8a10d5a4e0c334b01
https://github.com/galaxyproject/galaxy/commit/594e44b4fbca2a1d128f81c8a10d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/style/source_material/circle.py
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/parse_gx_xsd.py
M doc/patch.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/util/workflow_util.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/auth/pam_auth_helper.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/slideshow/build_slideshow.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M test/api/test_workflows.py
M test/api/workflows_format_2/main.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/workflows/test_modules.py
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge pull request #3170 from nsoranzo/dev
Fixes for pycodestyle 2.2.0
Commit: db63b131c1728493a87901764c102dbc47f74f3f
https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c10…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Fix styling, we don't need to force rounded edges here.
Commit: ca24098883fda1c35241d4c380f8b0765de7bb95
https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/style/less/dataset.less
M static/style/blue/base.css
Log Message:
-----------
Remove unused style, we can rely on the :last pseudoclasses for this.
Commit: f8974acba2884dc2fc1728aaa81021708ad05493
https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa810…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Fix styling when only one visualization type exists
Commit: 063bb61d07177f2736805521a888003d705e516e
https://github.com/galaxyproject/galaxy/commit/063bb61d07177f2736805521a888…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
add links to local tours to sample welcome
Commit: 2c756ff170da94b88829866f43082861a625b9fb
https://github.com/galaxyproject/galaxy/commit/2c756ff170da94b88829866f4308…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
drop leading slash to work with proxy prefix, thanks @dannon
Commit: a86a457230e87ab02de29bba13686ad0c1243a63
https://github.com/galaxyproject/galaxy/commit/a86a457230e87ab02de29bba1368…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
Merge pull request #3176 from martenson/add-tours-to-welcome
add links to local tours to sample welcome
Commit: dd556090c158b5062f0b7f6e0775281fcaabcb7e
https://github.com/galaxyproject/galaxy/commit/dd556090c158b5062f0b7f6e0775…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M test/manual/workflows_scaling.py
Log Message:
-----------
Fix import broken in b4c77b761799b3a8752a6fec500717b1a6f3818b
Commit: a8746c4f52295e5133950c0bffc3a9f07a2818ec
https://github.com/galaxyproject/galaxy/commit/a8746c4f52295e5133950c0bffc3…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Fix import order and Python3 compatibility for test/unit/
Commit: d48817adb17b914975c26b90a2dd17887b24744b
https://github.com/galaxyproject/galaxy/commit/d48817adb17b914975c26b90a2dd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M run.sh
Log Message:
-----------
Remove redundant .venv activation -- this is handled in common_startup
Commit: 72d360e942da2a614b7d74d3238d2ee0791a8141
https://github.com/galaxyproject/galaxy/commit/72d360e942da2a614b7d74d3238d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Change startup logic for .venv sourcing. If a .venv exists, use it. If not, if conda is there, use it. If no conda, create a .venv.
Commit: 7f5d9d2fbd745f2099be15de706112717f9e01f6
https://github.com/galaxyproject/galaxy/commit/7f5d9d2fbd745f2099be15de7061…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
More startup logic tweaks, .venv > conda > new_venv
Commit: 2f2d21aea25f45508bccf046f179041f3599c3b0
https://github.com/galaxyproject/galaxy/commit/2f2d21aea25f45508bccf046f179…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M test/manual/workflows_scaling.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
Log Message:
-----------
Merge pull request #3177 from nsoranzo/flake8-import-order
Fix import order and Python3 compatibility for test/unit/
Commit: 985bd0dffd779b55813f6dc1c6bae663e959bd9c
https://github.com/galaxyproject/galaxy/commit/985bd0dffd779b55813f6dc1c6ba…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M run.sh
Log Message:
-----------
Because common_startup is executed and not sourced, this block needs to remain in run.sh
Commit: 4e6e7d36f87249b93f4a49249e227409e629305e
https://github.com/galaxyproject/galaxy/commit/4e6e7d36f87249b93f4a49249e22…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Validate cycles and step size before building model for workflow execution
Commit: 45259b7f168f6c1eb17f4f6aec738ad9f9231518
https://github.com/galaxyproject/galaxy/commit/45259b7f168f6c1eb17f4f6aec73…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
Log Message:
-----------
Fix typo
Commit: 2f08dd72c3e028855b37dc1d113636dda2db9eab
https://github.com/galaxyproject/galaxy/commit/2f08dd72c3e028855b37dc1d1136…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M config/plugins/tours/core.galaxy_ui.yaml
Log Message:
-----------
Merge pull request #3184 from afgane/dev
Fix a typo in the intro tour
Commit: ac5b7efc5f88da9b337a8d98f36dbdbfe29bb3f6
https://github.com/galaxyproject/galaxy/commit/ac5b7efc5f88da9b337a8d98f36d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3130 from mvdbeek/fix_invalid_section_key
Update ToolPanelElements instance locally
Commit: 5028e2a25107e8f4cd2f136ab275853b5e31bb7f
https://github.com/galaxyproject/galaxy/commit/5028e2a25107e8f4cd2f136ab275…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M Makefile
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/tours/core.galaxy_ui.yaml
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
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M scripts/auth/pam_auth_helper.py
M scripts/bootstrap_history.py
R scripts/bootstrap_history_announce_template.rst
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/db_shell.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M setup.cfg
M static/maps/layout/menu.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
A static/maps/mvc/tool/tool-webhooks.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-tabs.js.map
A static/maps/mvc/ui/ui-thumbnails.js.map
A static/maps/mvc/webhooks.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
A static/scripts/mvc/tool/tool-webhooks.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
A static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/user/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/package.json
M test/qunit/tests/form_tests.js
M test/qunit/tests/ui_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional_tests.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into workflow_intermediates_ux
Commit: 953ee3259999f774887e97d5e72bccb1102540f5
https://github.com/galaxyproject/galaxy/commit/953ee3259999f774887e97d5e72b…
Author: Ignacio <ignacio.eguinoa(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
Log Message:
-----------
change parameters to samtools sort command (new samtools vers)
Commit: 5bb86a3b687732913dee746732060f973b622cff
https://github.com/galaxyproject/galaxy/commit/5bb86a3b687732913dee74673206…
Author: Ignacio <ignacio.eguinoa(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
Log Message:
-----------
correct indentation
Commit: e5b69a711d14fa8e8876041f92160db19da3e9bf
https://github.com/galaxyproject/galaxy/commit/e5b69a711d14fa8e8876041f9216…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/scripts/mvc/tool/tool-form-workflow.js
M static/style/blue/base.css
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge pull request #2966 from dannon/workflow_intermediates_ux
Change wording to be more clear about how workflow output cleanup wor…
Commit: efde00d80a916afc20869608a7a1922249581a62
https://github.com/galaxyproject/galaxy/commit/efde00d80a916afc20869608a7a1…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
Log Message:
-----------
Handle samtools 0.x
Commit: 0b8fc7c8cca4b7374f12932b26ef3d854e2d8491
https://github.com/galaxyproject/galaxy/commit/0b8fc7c8cca4b7374f12932b26ef…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge remote-tracking branch 'guerler/validate_workflow' into dev
Commit: 31b73fd5869f1c3ae968fb29773cf1631a3f5843
https://github.com/galaxyproject/galaxy/commit/31b73fd5869f1c3ae968fb29773c…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #3180 from dannon/venv_over_conda
Prefer existing .venv over conda, when both are available.
Commit: 92105d99fae6ec892f2eb6eb60c31d68196b061a
https://github.com/galaxyproject/galaxy/commit/92105d99fae6ec892f2eb6eb60c3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
Log Message:
-----------
Merge pull request #2818 from erasche/rstudio-1610
Return of RStudio
Commit: 592f15c7b5da3f962dda9f98cb978e5c5c6b4a1d
https://github.com/galaxyproject/galaxy/commit/592f15c7b5da3f962dda9f98cb97…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
A test/functional/tools/sam_to_bam.xml
Log Message:
-----------
Add sam-to-bam conversion test tool
Commit: 0b395a7fb3aaebf5fa3a0448338df73c8774e388
https://github.com/galaxyproject/galaxy/commit/0b395a7fb3aaebf5fa3a0448338d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Slight clarification of run.sh messaging when using conda.
Commit: 164a0ad20cbbd55b40583c633c1c52dde9ecb7ba
https://github.com/galaxyproject/galaxy/commit/164a0ad20cbbd55b40583c633c1c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #3188 from dannon/startup_output_tweaks
Slight clarification of run.sh messaging when using conda.
Commit: 8ace021c0af79e5d325d6a590f525bce881715f8
https://github.com/galaxyproject/galaxy/commit/8ace021c0af79e5d325d6a590f52…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
Log Message:
-----------
Single quote variables in sam-to-bam conversion
Commit: d8c75e2dffbfa754eda4fae4c6d3365d42278a4c
https://github.com/galaxyproject/galaxy/commit/d8c75e2dffbfa754eda4fae4c6d3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/sam_to_bam.py
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
A test/functional/tools/sam_to_bam.xml
Log Message:
-----------
Merge pull request #3187 from mvdbeek/samtools_1_3_fix
Make sam to bam converter tool compatible with samtools >= 1.3
Commit: 9d45f1e48a4321d5df0543bcfcf2994affa35612
https://github.com/galaxyproject/galaxy/commit/9d45f1e48a4321d5df0543bcfcf2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 16.10.rc1
Commit: 6fd58afa6daf708f373513782ac907c154c266da
https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-17 (Thu, 17 Nov 2016)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Merge pull request #3191 from dannon/version-16.10
Update version to 16.10.rc1
Commit: 5c4ac18b44263df72b25826c03d8c2509ca68a1a
https://github.com/galaxyproject/galaxy/commit/5c4ac18b44263df72b25826c03d8…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-18 (Fri, 18 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/tool/tools.js
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
remove unused override
this caused Help/Search to point at /root/tool_search
Commit: 3f27777e76086ac94c95003882bb82003c277b4e
https://github.com/galaxyproject/galaxy/commit/3f27777e76086ac94c95003882bb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-18 (Fri, 18 Nov 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/tool/tools.js
M lib/galaxy/webapps/galaxy/controllers/root.py
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
Log Message:
-----------
Merge pull request #3198 from martenson/fix-search-config
[16.10] remove unused (and unintended) config override
Commit: 548d3e6f05b722301deefada71d5dafda81a1881
https://github.com/galaxyproject/galaxy/commit/548d3e6f05b722301deefada71d5…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
Log Message:
-----------
Fixes for deleting histories broken in 1cc57b1eb2c295dbd68837c864740b6ff079b83d
Commit: 5ba820116365ad42dd24e099b747b40d399e6dee
https://github.com/galaxyproject/galaxy/commit/5ba820116365ad42dd24e099b747…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M static/maps/mvc/history/options-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Pack scripts
Commit: aadc14d967c30683a10e68df61b82bb4f805de98
https://github.com/galaxyproject/galaxy/commit/aadc14d967c30683a10e68df61b8…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/maps/mvc/history/options-menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Merge pull request #3203 from blankenberg/fix_history_delete_16.10
[16.10] Fixes for deleting histories
Commit: 74d8faac9f07407ac9df344a78c9ecb06c178f93
https://github.com/galaxyproject/galaxy/commit/74d8faac9f07407ac9df344a78c9…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Change 'History Actions' to 'Current History' in history options menu.
as it was before 1cc57b1eb2c295dbd68837c864740b6ff079b83d.
Commit: ec08ec60bb4dadaf6f8759f9dce79f764f26c909
https://github.com/galaxyproject/galaxy/commit/ec08ec60bb4dadaf6f8759f9dce7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-21 (Mon, 21 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/options-menu.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Merge pull request #3205 from blankenberg/history-current-options-name_16.10
[16.10] Change 'History Actions' to 'Current History' in history options menu.
Commit: a9dab631fb00252ac122ea297262e89f63887019
https://github.com/galaxyproject/galaxy/commit/a9dab631fb00252ac122ea297262…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/form/form-section.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
Log Message:
-----------
Preserve custom event handler for form inputs
Commit: 0b2d0c1746c9b7d7cc5781fedc5c6a02af3bdfdb
https://github.com/galaxyproject/galaxy/commit/0b2d0c1746c9b7d7cc5781fedc5c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-22 (Tue, 22 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M static/maps/mvc/form/form-section.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
Log Message:
-----------
Merge pull request #3210 from guerler/fix_output_label_handler
[16.10] Preserve custom event handler for form inputs
Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb
https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes.
Commit: 9a2bae7381b1ee8e2411681a76d75767b05ceffe
https://github.com/galaxyproject/galaxy/commit/9a2bae7381b1ee8e2411681a76d7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
simplify the UI of deps installation
by hiding the details under toggle button
Commit: 068ee6bd0ceb942ec67e634a7e6e434314cbe7fe
https://github.com/galaxyproject/galaxy/commit/068ee6bd0ceb942ec67e634a7e6e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
Log Message:
-----------
fix install repo test
Commit: 29cf7187233bbd031f07df4584f1bef55de612e4
https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Minor styling tweaks -- todo: swap from inline to class-based.
Commit: 706bc3fbb118087cc057e6559e0262a6aca31127
https://github.com/galaxyproject/galaxy/commit/706bc3fbb118087cc057e6559e02…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
Log Message:
-----------
fix test and hide shed_conf select udner details
Commit: 73d010efa4236ed8ef0e46bb10d5e39233ae2d6b
https://github.com/galaxyproject/galaxy/commit/73d010efa4236ed8ef0e46bb10d5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
fix another test
Commit: 4b794729b0cfd347d189a9a1e62273ab1788bc3e
https://github.com/galaxyproject/galaxy/commit/4b794729b0cfd347d189a9a1e622…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
fix a bug that renders conda dependency selection everytime
Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7
https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/style/blue/base.css
Log Message:
-----------
Standard styles inclusion in .less, more styling to match rounded edges and spacing.
Commit: 94edc94b73e047612ae51ca2e075f17ac8e238bb
https://github.com/galaxyproject/galaxy/commit/94edc94b73e047612ae51ca2e075…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Add cached dependency manager
Similar to https://github.com/galaxyproject/galaxy/pull/2986, implement
a mechanism that allows tool dependencies to be cached.
If the `use_cached_dependency_manager` option is set to True in
galaxy.ini, we build a hash of the combination of a tools' requirements,
and store the resulting environment in a directory specified by the
`tool_dependency_cache_dir` option in galaxy.ini.
Commit: 0a9b6d8755dee530232ab893a3bad199407aa0bc
https://github.com/galaxyproject/galaxy/commit/0a9b6d8755dee530232ab893a3ba…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
Log Message:
-----------
Better phrasing of cache options in galaxy.ini.sample (Thanks @nsoranzo)
Commit: 2b1765751b29008aecbd782f28269ac4e63db239
https://github.com/galaxyproject/galaxy/commit/2b1765751b29008aecbd782f2826…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Rework cached dependencies to be more robust
to updates or changes in depedencies, folder structure and resolver
configuration. Instead of hashing name, type and version of a
dependency, hash the json representation of the dependencies returned by
the dependency resolver, which include the path to the environment and
the depedency type. This is only applied to resolvers whose cacheable
attribute is set to True (conda-only, currently).
Commit: f919a98601252ab8f87bffff6e449105e770aadf
https://github.com/galaxyproject/galaxy/commit/f919a98601252ab8f87bffff6e44…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Build dependency cache at install time
and only activate cached environments if they exist.
Commit: 82f30e7645156b5f35c2b4cd77314e6275663979
https://github.com/galaxyproject/galaxy/commit/82f30e7645156b5f35c2b4cd7731…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/requirements.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Only attempt to build cache once per install
and override __eq__ for ToolRequirement, to simplify
checking if ToolRequirements are already installed/cached.
Commit: 64bc9241ed785d4d552c5fac21cd412558c54567
https://github.com/galaxyproject/galaxy/commit/64bc9241ed785d4d552c5fac21cd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Fix NameError
Commit: cf769dd09deb73624b22628208fa103cc4f27150
https://github.com/galaxyproject/galaxy/commit/cf769dd09deb73624b22628208fa…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add API to install resolver tool dependencies
and to build a tool dependency cache (if activated in galaxy.ini).
An example to install dependencies for the twobit converter:
```
import bioblend.galaxy
url = 'http://localhost:8080/'
api_key = 'admin_api_key'
tool_id = 'CONVERTER_fasta_to_2bit'
endpoint = "api/tools/%s/install_dependencies" % tool_id
gi = bioblend.galaxy.GalaxyInstance(url, api_key)
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
If `use_cached_dependency_manager` is activated in the galaxy.ini,
a cached environment can be built like this:
```
endpoint = "api/tools/%s/build_dependency_cache" % tool_id
gi.make_post_request("/".join((url, endpoint)), payload={'id': tool_id})
```
Commit: cc7cd47ef54a09efbf8272d1e024f6f2ac92594b
https://github.com/galaxyproject/galaxy/commit/cc7cd47ef54a09efbf8272d1e024…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M test/integration/test_resolvers.py
Log Message:
-----------
Add integration test-case for install tool dependency API endpoint
Commit: f10fd793a68ed9413bec708daa48cef65769d09f
https://github.com/galaxyproject/galaxy/commit/f10fd793a68ed9413bec708daa48…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
Log Message:
-----------
Install the correct converter dependency
Commit: 045a2f0d471f7b4186aff625f3cea9abfa549fa2
https://github.com/galaxyproject/galaxy/commit/045a2f0d471f7b4186aff625f3ce…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
Log Message:
-----------
Add `force_rebuild` param to build_dependency_cache
This will remove a pre-existing cached dependency directory.
Commit: 16b49d9140edbf116f83b51b957cd61c4f2d91df
https://github.com/galaxyproject/galaxy/commit/16b49d9140edbf116f83b51b957c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Add dependency_resolvers/clean endpoint
Commit: 1efd4d4b3b99ec40071aa4d6fb7cf4030c51e2e0
https://github.com/galaxyproject/galaxy/commit/1efd4d4b3b99ec40071aa4d6fb7c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
add a conda clean function to remove downloaded tarballs after installation
Commit: 2a4ccac4039342c98d71bc72177aa951db6c4ba1
https://github.com/galaxyproject/galaxy/commit/2a4ccac4039342c98d71bc72177a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/buildapp.py
M test/integration/test_resolvers.py
Log Message:
-----------
Connect `clean` endpoint properly and add `-y` to exec_clean
Commit: e3f8b724648cee51636502959096adba88045e14
https://github.com/galaxyproject/galaxy/commit/e3f8b724648cee51636502959096…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
Log Message:
-----------
Merge pull request #3226 from martenson/16-10-install-ux
[16.10] admin installation ux
Commit: d6f0e6b37c318a0202e0e266828e6325100cab19
https://github.com/galaxyproject/galaxy/commit/d6f0e6b37c318a0202e0e266828e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/tool_shed/galaxy_install/install_manager.py
M test/integration/test_resolvers.py
Log Message:
-----------
Merge pull request #3227 from mvdbeek/cached_deps_16.10
[16.10] Backport #3106 and #3222: Cached conda environments and API to manage them
Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8
https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/parse_gx_xsd.py
M doc/patch.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/version.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/workflow_util.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/auth/pam_auth_helper.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/slideshow/build_slideshow.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tools.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/webapps/galaxy/workflow/editor.mako
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
M test/api/test_workflows.py
M test/api/workflows_format_2/main.py
M test/base/api_asserts.py
M test/base/driver_util.py
A test/functional/tools/sam_to_bam.xml
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history
Commit: a26568bdfaefc5748ff3b2385fa9424ece6c652c
https://github.com/galaxyproject/galaxy/commit/a26568bdfaefc5748ff3b2385fa9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M tox.ini
Log Message:
-----------
Pin flake8 and flake8-import-order
Do not pin when forward-merging to dev branch!
Commit: 888a8f91537e22dcbdea174a65eaecbced9ea8a8
https://github.com/galaxyproject/galaxy/commit/888a8f91537e22dcbdea174a65ea…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-11-30 (Wed, 30 Nov 2016)
Changed paths:
M tox.ini
Log Message:
-----------
Merge pull request #3232 from nsoranzo/release_16.10_pin_flake8
[16.10] Pin flake8 and flake8-import-order
Commit: bab709c755ef2ba83849c9457f9558d79a11eaf3
https://github.com/galaxyproject/galaxy/commit/bab709c755ef2ba83849c9457f95…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-12-03 (Sat, 03 Dec 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Request information about tool dependencies from toolshed and make available in prepare_for_install
Commit: 72f417ef977030ce092219b7565f2cb6650e5a2c
https://github.com/galaxyproject/galaxy/commit/72f417ef977030ce092219b7565f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-12-03 (Sat, 03 Dec 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Display requirement status on TS install
This commit displays tool requirements as defined in the tool xml during
the install confirmation dialog. If a tool dependency is defined in the
tool XML, but not in a tool_dependencies.xml, a warning is shown if
conda is not activated.
This should close #3257.
Commit: f20c478bd963c9eb907b711af659f17ef47c171f
https://github.com/galaxyproject/galaxy/commit/f20c478bd963c9eb907b711af659…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-12-03 (Sat, 03 Dec 2016)
Changed paths:
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
Log Message:
-----------
Use Tool Shed instead of toolshed
Commit: 622f2997376bceb30b822f6c5f1b3a0096e5e2f9
https://github.com/galaxyproject/galaxy/commit/622f2997376bceb30b822f6c5f1b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-05 (Mon, 05 Dec 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/tool_shed/util/shed_util_common.py
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/webapps/tool_shed/repository/common.mako
Log Message:
-----------
Merge pull request #3262 from mvdbeek/conda_only_improvements
[16.10] Display tool requirements for conda-only tools
Commit: a84601ba80cb8620a396e740e9a69f3d6f1dfd37
https://github.com/galaxyproject/galaxy/commit/a84601ba80cb8620a396e740e9a6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-05 (Mon, 05 Dec 2016)
Changed paths:
A doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
A doc/source/releases/17.01_announce.rst
M scripts/bootstrap_history.py
Log Message:
-----------
Add 16.10 release notes.
Commit: 7fa10aa907ad6527f9e71a4d661281d21ac9150c
https://github.com/galaxyproject/galaxy/commit/7fa10aa907ad6527f9e71a4d6612…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2016-12-06 (Tue, 06 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Simplify dependency list for cached environemnts (many thanks @nsoranzo)
Commit: d0ad2ae1ce296e41e88264b0a770bf9c176db814
https://github.com/galaxyproject/galaxy/commit/d0ad2ae1ce296e41e88264b0a770…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-12-06 (Tue, 06 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Merge pull request #3272 from mvdbeek/fix_superfluous_brackets
[16.10] Simplify dependency list for cached environemnts (many thanks @nsoranzo)
Commit: a1e3965eaf7e850486d289d1a2026877177b3c27
https://github.com/galaxyproject/galaxy/commit/a1e3965eaf7e850486d289d1a202…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-06 (Tue, 06 Dec 2016)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
Fix tour URLs in welcome
Commit: 8a5ff5df21efc6db7d2df47171f7cbad5cb1f608
https://github.com/galaxyproject/galaxy/commit/8a5ff5df21efc6db7d2df47171f7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-06 (Tue, 06 Dec 2016)
Changed paths:
M static/welcome.html.sample
Log Message:
-----------
Merge pull request #3277 from dannon/fix_tour_welcome_1610
[16.10] port Fix tour URLs in welcome
Commit: 8766e125091d0a5a83a0fd4daf274fe93551a443
https://github.com/galaxyproject/galaxy/commit/8766e125091d0a5a83a0fd4daf27…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
Log Message:
-----------
Escape filename in upload dialog, default and composite. Pointed out by David Wyde.
Commit: 13ab07030c8ffa5012a123671c2ab450bf14c40b
https://github.com/galaxyproject/galaxy/commit/13ab07030c8ffa5012a123671c2a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/upload/default/default-row.js
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Use consistent spacing.
Commit: 75d327f165c730f95e181a2feff1db64074ab3e6
https://github.com/galaxyproject/galaxy/commit/75d327f165c730f95e181a2feff1…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
Log Message:
-----------
Merge pull request #3278 from dannon/upload_escape_filename
[16.10] Escape filename in upload dialog, default and composite.
Commit: f6b94dc465a41e0ce25cd0d38b8cfa81ab4c5254
https://github.com/galaxyproject/galaxy/commit/f6b94dc465a41e0ce25cd0d38b8c…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Fix for ToolShed install when copied sample data target exists, but is broken symlink.
Commit: 70fc43b24090e537479a74b34a7ff9bc4e43de84
https://github.com/galaxyproject/galaxy/commit/70fc43b24090e537479a74b34a7f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Merge pull request #3279 from blankenberg/16.10_ts_install_broken_symlink
[16.10] Fix for ToolShed install when copied sample data target exists, but is broken symlink.
Commit: 128a3174ebc425dfe750767eef40374d0b282448
https://github.com/galaxyproject/galaxy/commit/128a3174ebc425dfe750767eef40…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M doc/Makefile
Log Message:
-----------
Use OSX-compatible sed syntax
Commit: d0f39ceff51843a95048dfdaf49035d07ce75c1d
https://github.com/galaxyproject/galaxy/commit/d0f39ceff51843a95048dfdaf490…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
A doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
A doc/source/releases/17.01_announce.rst
M scripts/bootstrap_history.py
Log Message:
-----------
Merge pull request #3270 from jmchilton/16.10_release_notes_0
[16.10] Add 16.10 release notes.
Commit: 3e0e96657d765f4023bb6801ace2e96a1ffc4505
https://github.com/galaxyproject/galaxy/commit/3e0e96657d765f4023bb6801ace2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M doc/source/admin/index.rst
M doc/source/admin/webhooks.rst
M doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
Log Message:
-----------
add work on release notes 16.10, improve docs for webhooks
Conflicts:
doc/source/releases/16.10.rst
doc/source/releases/16.10_announce.rst
Commit: 739fb59cba5b7747a32e685a3632f96effad4c11
https://github.com/galaxyproject/galaxy/commit/739fb59cba5b7747a32e685a3632…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M doc/source/admin/webhooks.rst
Log Message:
-----------
fix the fix
Commit: 5784a838a554f8dcf9e132e26be01240a37a3e65
https://github.com/galaxyproject/galaxy/commit/5784a838a554f8dcf9e132e26be0…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M doc/source/releases/16.10.rst
Log Message:
-----------
fix bad merge
Commit: 83de83e7edc230d7f9841a6d9770d87d0c89d06f
https://github.com/galaxyproject/galaxy/commit/83de83e7edc230d7f9841a6d9770…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M doc/source/admin/index.rst
M doc/source/admin/webhooks.rst
M doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
Log Message:
-----------
Merge pull request #3282 from martenson/release_16.10
[16.10] work on release notes 16.10
Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3
https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Don't rely on complex, absolute selector, use local element.find()
Commit: e3fbbc52b999f9e25e7b02c4edf44ddd43a63622
https://github.com/galaxyproject/galaxy/commit/e3fbbc52b999f9e25e7b02c4edf4…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M doc/source/releases/16.10_announce.rst
Log Message:
-----------
add small touches to release notes
Commit: c01e25ddf8854e20a96040b3c8616136ec517574
https://github.com/galaxyproject/galaxy/commit/c01e25ddf8854e20a96040b3c861…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M doc/source/releases/16.10_announce.rst
Log Message:
-----------
missing articles
Commit: 2cbf9a9138b6fb89d06f41398539908a5df4585e
https://github.com/galaxyproject/galaxy/commit/2cbf9a9138b6fb89d06f41398539…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M doc/source/releases/16.10_announce.rst
Log Message:
-----------
Merge pull request #3284 from martenson/notes-tinies
[16.10] add small touches to release notes
Commit: 4431d735c8908b19bbcd1ca594ec1a194cf4d299
https://github.com/galaxyproject/galaxy/commit/4431d735c8908b19bbcd1ca594ec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
Log Message:
-----------
Extend list of tabular datatypes for bar diagrams
Commit: c315f1d74bc8b4c4c2e5d6f0d4acd02d64b89e43
https://github.com/galaxyproject/galaxy/commit/c315f1d74bc8b4c4c2e5d6f0d4ac…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
Log Message:
-----------
Upload file escaping backport.
Commit: 13ae374f84926e71b3dde7080d8d74ad443916e3
https://github.com/galaxyproject/galaxy/commit/13ae374f84926e71b3dde7080d8d…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M doc/Makefile
A doc/fix_schema_rst.sh
Log Message:
-----------
Move sed commands to a script to resolve interferences with Make
which happen only under OSX
Commit: ca99753590abf62df2c34e80a87b1ae2ec3424e2
https://github.com/galaxyproject/galaxy/commit/ca99753590abf62df2c34e80a87b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-12-08 (Thu, 08 Dec 2016)
Changed paths:
M doc/Makefile
A doc/fix_schema_rst.sh
Log Message:
-----------
Merge pull request #3281 from nsoranzo/release_16.10_fix_doc_Makefile
[16.10] Use OSX-compatible sed syntax
Commit: 22687410c4829dd9a0e44f55ee93b1020c8eab20
https://github.com/galaxyproject/galaxy/commit/22687410c4829dd9a0e44f55ee93…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Ensure Conda prefix and cached environment are absolute paths
Otherwise when Conda commands are executed from the job working
directory, they will break.
Commit: 879e3d69606e1a4b98bd34f75bf905b9da6edcfa
https://github.com/galaxyproject/galaxy/commit/879e3d69606e1a4b98bd34f75bf9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Skip building cache if force_rebuild is False
Also:
- re-raise exception if rmtree() fails
- change hash(ed)_requirements to hash(ed)_dependencies
Commit: 7c9d9d2231ecc113f7d69737a4aa4ec140b7e48c
https://github.com/galaxyproject/galaxy/commit/7c9d9d2231ecc113f7d69737a4aa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Apply a fix similar to 36134bca694c9dc6b2584fb661dfbce4ddb793e6 for the workflow editor. Not ideal, but this is old code we're replacing as the editor is overhauled.
Commit: 602f2f2f1d431306c9aa64a6818c8feddaabb261
https://github.com/galaxyproject/galaxy/commit/602f2f2f1d431306c9aa64a6818c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/default/default-row.js
Log Message:
-----------
Merge pull request #3292 from dannon/backport_upload_fn_escape
[16.07] Upload file escaping backport.
Commit: d6d2a12ec071e6cfa297944917ed201895f56332
https://github.com/galaxyproject/galaxy/commit/d6d2a12ec071e6cfa297944917ed…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-09 (Fri, 09 Dec 2016)
Changed paths:
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge branch 'release_16.07' into release_16.10
Conflicts:
client/galaxy/scripts/mvc/upload/composite/composite-row.js
client/galaxy/scripts/mvc/upload/default/default-row.js
static/maps/mvc/upload/composite/composite-row.js.map
static/maps/mvc/upload/default/default-row.js.map
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
static/scripts/bundled/login.bundled.js.map
static/scripts/mvc/upload/composite/composite-row.js
static/scripts/mvc/upload/default/default-row.js
Commit: 5a7f9e876e28ea773b79af9bbb887de7cff4aaa7
https://github.com/galaxyproject/galaxy/commit/5a7f9e876e28ea773b79af9bbb88…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Correctly update TS repo status
Execute build_dependency_cache() only if using a cached dependency
manager.
Set tool versions only if the TS repo contains tools.
Raise exception if fetch_tool_versions() fails, previously the
error message never reached the UI.
Commit: 9dda310cd35e18c3ef86c5b09a021fc359fe5011
https://github.com/galaxyproject/galaxy/commit/9dda310cd35e18c3ef86c5b09a02…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge pull request #3296 from dannon/workflow_editor_toolsearch_messagebox_fix
[16.10] Workflow editor 'messagebox' fix.
Commit: 22c7fcf3fff19ed9f271ada3cd8c007a96444768
https://github.com/galaxyproject/galaxy/commit/22c7fcf3fff19ed9f271ada3cd8c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Merge pull request #3295 from nsoranzo/release_16.10_tool_install_fixes
[16.10] Tool install fixes
Commit: 2c833499b130aca72ab78d112692f2a9f0d4d9e6
https://github.com/galaxyproject/galaxy/commit/2c833499b130aca72ab78d112692…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-11 (Sun, 11 Dec 2016)
Changed paths:
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
Log Message:
-----------
Merge pull request #3287 from guerler/fix_chart_datatypes
[16.10] Rely on tabular subclass matching through vizframework layer
Commit: bb8a5a2215c2fce0e1c5fb69f4665358d72905f6
https://github.com/galaxyproject/galaxy/commit/bb8a5a2215c2fce0e1c5fb69f466…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-13 (Tue, 13 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/commands.py
Log Message:
-----------
[16.10] Revert commands.shell changes from galaxyproject/galaxy#3129.
It seems like people prefer to see the interactive shell https://github.com/galaxyproject/galaxy/issues/3259. See follow up here https://github.com/galaxyproject/galaxy/issues/3309.
This also fixes an issue caused by the change of the constructor interface for CommandLineException in galaxyproject/galaxy#3129.
Commit: 329108f81021e779db43a6a5c3b2808fd6c14b42
https://github.com/galaxyproject/galaxy/commit/329108f81021e779db43a6a5c3b2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/tools/deps/commands.py
Log Message:
-----------
Merge pull request #3310 from jmchilton/shell_fix
[16.10] Revert commands.shell changes from galaxyproject/galaxy#3129.
Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb
https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming /
Commit: d2ab7e701c87f4292b655893103c7842900a47b5
https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/extra-information.js.map
A static/maps/mvc/user/manage-user-information.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
M static/style/blue/base.css
Log Message:
-----------
build the client
Commit: c1e3087ca35dbca1b0328954fe4769d666d3f934
https://github.com/galaxyproject/galaxy/commit/c1e3087ca35dbca1b0328954fe47…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Fix an ACE vulnerability with gff filter tools. Thanks to David Wyde for
the disclosure.
Commit: 9ee3d01c301ca067f7b94ee3c75bd784fafc4572
https://github.com/galaxyproject/galaxy/commit/9ee3d01c301ca067f7b94ee3c75b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_14.10' into release_15.01
Commit: da7afb4e22f352c40a53da8b3e18319ed7aeb844
https://github.com/galaxyproject/galaxy/commit/da7afb4e22f352c40a53da8b3e18…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.01' into release_15.03
Commit: 7c443eda567ece12fb90330e131e7f97c7b63ba2
https://github.com/galaxyproject/galaxy/commit/7c443eda567ece12fb90330e131e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.03' into release_15.05
Commit: 790e60af60093dcb8e26f093c3a87903605da206
https://github.com/galaxyproject/galaxy/commit/790e60af60093dcb8e26f093c3a8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.05' into release_15.07
Commit: 95daf69b372fa829325be561dc0a9907da0bea81
https://github.com/galaxyproject/galaxy/commit/95daf69b372fa829325be561dc0a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.07' into release_15.10
Commit: 4c07734f57453581666fd3994c44d583f3e319b9
https://github.com/galaxyproject/galaxy/commit/4c07734f57453581666fd3994c44…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_15.10' into release_16.01
Commit: 4cf70aea79772780b49dcdff08d63f40ca75ac6d
https://github.com/galaxyproject/galaxy/commit/4cf70aea79772780b49dcdff08d6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_16.01' into release_16.04
Commit: 22fda449f9d4ff2ed21fe4e39080456120aaf95e
https://github.com/galaxyproject/galaxy/commit/22fda449f9d4ff2ed21fe4e39080…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_16.04' into release_16.07
Commit: 42cda969281c2d3e2918eb0d376415154e22d1db
https://github.com/galaxyproject/galaxy/commit/42cda969281c2d3e2918eb0d3764…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
Log Message:
-----------
Merge branch 'release_16.07' into release_16.10
Commit: 5c01c01791ad79bef23388b6892de974ad7b6323
https://github.com/galaxyproject/galaxy/commit/5c01c01791ad79bef23388b6892d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
Log Message:
-----------
Add security disclosure to release notes
Commit: c1397908cd1fc81b294849008b1e5ec1b1381660
https://github.com/galaxyproject/galaxy/commit/c1397908cd1fc81b294849008b1e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 16.10
Commit: 378ed53a33eee02c3620310c7245e7a85d279427
https://github.com/galaxyproject/galaxy/commit/378ed53a33eee02c3620310c7245…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
M client/bower.json
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
A client/galaxy/scripts/libs/jquery.complexify.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/base-mvc.js
A client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
A client/galaxy/scripts/mvc/history/history-preferences.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/ui/search-input.js
M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
A client/galaxy/style/less/collection.less
R client/galaxy/style/less/collections.less
A client/galaxy/style/less/dataset.less
A client/galaxy/style/less/flex.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/list-item.less
M client/galaxy/style/less/ui.less
A client/galaxy/style/less/ui/error-modal.less
M client/galaxy/style/less/ui/search-input.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
M client/grunt-tasks/install-libs.js
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
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R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
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A static/maps/mvc/user/extra-information.js.map
A static/maps/mvc/user/manage-user-information.js.map
A static/maps/mvc/webhooks.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/ui/search-input.js.map
M static/maps/utils/ajax-queue.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/panel.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
A static/scripts/libs/jquery.complexify.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/raven.js
M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
A static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
A static/scripts/mvc/history/history-preferences.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
A static/scripts/mvc/tool/tool-webhooks.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
A static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/ui/search-input.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M static/style/blue/bootstrap-tour.css
M static/style/blue/jquery.rating.css
R static/style/blue/tool_menu.css
M static/welcome.html.sample
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/show_params.mako
M templates/user/change_password.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/admin/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/index.mako
R templates/webapps/galaxy/workflow/missing_tools.mako
R templates/webapps/galaxy/workflow/myexp_export_content.mako
R templates/webapps/galaxy/workflow/rename.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/reports/index.mako
M templates/webapps/tool_shed/admin/index.mako
M templates/webapps/tool_shed/group/index.mako
M templates/webapps/tool_shed/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
M test/api/helpers.py
A test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
A test/casperjs/api-batch-tests.js
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
R test/functional/tools/multi_page.xml
A test/functional/tools/sam_to_bam.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_directory.xml
A test/functional/tools/tool_provided_metadata_1.xml
A test/functional/tools/tool_provided_metadata_2.xml
A test/functional/tools/tool_provided_metadata_3.xml
M test/functional/tools/validation_repeat.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/package.json
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_objectstore.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'release_16.10'
Compare: https://github.com/galaxyproject/galaxy/compare/d10758a4f22d...378ed53a33ee
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ac581a5453e6f43a4900d55d67a3c1bd75081f47
https://github.com/galaxyproject/galaxy/commit/ac581a5453e6f43a4900d55d67a3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M run_tests.sh
M test/base/api.py
M test/base/integration_util.py
M test/integration/test_resolvers.py
Log Message:
-----------
Improved documentation and design of integration tests.
- Allow running through ``run_tests.sh``.
- Enable more verbose test errors for Conda tests.
- Refactor how integration tests depend on API testing (use a Mixin instead of subclassing conceptually conflicting TestCase classes).
Commit: 00c6ee17b7f742efdd895fae44771edacba77c4b
https://github.com/galaxyproject/galaxy/commit/00c6ee17b7f742efdd895fae4477…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M .ci/jenkins/integration/run_tests.sh
Log Message:
-----------
Fix Jenkins script test for integration tests.
Commit: b78287f1508db2c06f0c309ed8d3747adb4d17fa
https://github.com/galaxyproject/galaxy/commit/b78287f1508db2c06f0c309ed8d3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M test/base/driver_util.py
M test/base/interactor.py
M test/functional/test_toolbox.py
A test/integration/retry_jobs_job_conf.xml
A test/integration/retry_jobs_job_resource_parameters_conf.xml
A test/integration/retry_runner.py
A test/integration/test_retry_jobs.py
M test/unit/jobs/test_mapper.py
Log Message:
-----------
Integration test for advanced job runner stuff.
Set of test cases that cover job resource handlers and resubmit job destinations.
Commit: 0559cff6e94b250ddd98275b119ab51b36491e34
https://github.com/galaxyproject/galaxy/commit/0559cff6e94b250ddd98275b119a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
A test/integration/resubmission_job_conf.xml
A test/integration/resubmission_job_resource_parameters_conf.xml
A test/integration/resubmission_rules/__init__.py
A test/integration/resubmission_rules/rules.py
A test/integration/resubmission_runners.py
R test/integration/retry_jobs_job_conf.xml
R test/integration/retry_jobs_job_resource_parameters_conf.xml
R test/integration/retry_runner.py
A test/integration/test_job_resubmission.py
R test/integration/test_retry_jobs.py
Log Message:
-----------
Implement resubmit on unknown failures.
Commit: 7d52b28ab2ab0314cd4fa31108a6750cb9750ef3
https://github.com/galaxyproject/galaxy/commit/7d52b28ab2ab0314cd4fa31108a6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M test/integration/resubmission_job_conf.xml
M test/integration/test_job_resubmission.py
Log Message:
-----------
Allow expressions in job_conf resubmission conditions.
Since we allow dynamic job runners clearly job_conf.xml must be considered a trusted document. Still I know that some are uneasy with eval generally so I only allow a very safe subset of Python expressions in this job_conf document.
Commit: 949d1224892861bd27207dd0799e2b356576c2cb
https://github.com/galaxyproject/galaxy/commit/949d1224892861bd27207dd0799e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/handler.py
Log Message:
-----------
Fix preservation of resubmits for resubmitted jobs.
Create an abstraction for the explicit handling of resubmits that is done during job recovery at startup.
xref https://github.com/galaxyproject/galaxy/commit/5539a083e21b601bfd2f87fa3417…
Commit: 7e338d790964f594ae67b33e6a72e1777e774b8c
https://github.com/galaxyproject/galaxy/commit/7e338d790964f594ae67b33e6a72…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/model/__init__.py
M test/integration/resubmission_job_conf.xml
M test/integration/resubmission_runners.py
M test/integration/test_job_resubmission.py
Log Message:
-----------
Add attempt to resubmission expression language.
Commit: 325b0354754815d32ed458d212d8c1c192630b0b
https://github.com/galaxyproject/galaxy/commit/325b0354754815d32ed458d212d8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M test/integration/resubmission_job_conf.xml
Log Message:
-----------
Add a self re-submission test.
Commit: 18eb1c8d0e4c3f7616d44fd177c90943695b7053
https://github.com/galaxyproject/galaxy/commit/18eb1c8d0e4c3f7616d44fd177c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/model/__init__.py
M test/integration/resubmission_job_conf.xml
M test/integration/resubmission_job_resource_parameters_conf.xml
M test/integration/resubmission_runners.py
M test/integration/test_job_resubmission.py
Log Message:
-----------
Add seconds_running and seconds_since_queued to condition expression langauge.
Commit: 334dfe1b116775466ef772a9d7a98d6247959ed0
https://github.com/galaxyproject/galaxy/commit/334dfe1b116775466ef772a9d7a9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/model/__init__.py
M test/integration/resubmission_job_conf.xml
M test/integration/resubmission_runners.py
M test/integration/test_job_resubmission.py
Log Message:
-----------
Allow (and test) using expressions in job re-submission delays.
So you can backoff re-submission with ``delay="attempt * 30"`` for instance - which will cause a re-submission delay to increase by 30 seconds for each resubmission of a job.
Commit: 521a585a23459714e9723903363ffa495918cc60
https://github.com/galaxyproject/galaxy/commit/521a585a23459714e9723903363f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M lib/galaxy/jobs/runners/local.py
M test/integration/resubmission_runners.py
Log Message:
-----------
Two lint fixes for #3291.
Commit: 498dddb03fe33df71ec887a9c53311ce53069e31
https://github.com/galaxyproject/galaxy/commit/498dddb03fe33df71ec887a9c533…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M .ci/jenkins/integration/run_tests.sh
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/model/__init__.py
M run_tests.sh
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/functional/test_toolbox.py
A test/integration/resubmission_job_conf.xml
A test/integration/resubmission_job_resource_parameters_conf.xml
A test/integration/resubmission_rules/__init__.py
A test/integration/resubmission_rules/rules.py
A test/integration/resubmission_runners.py
A test/integration/test_job_resubmission.py
M test/integration/test_resolvers.py
M test/unit/jobs/test_mapper.py
Log Message:
-----------
Merge pull request #3291 from jmchilton/integration_tests_0
Ready Integration Testing for Prime Time
Compare: https://github.com/galaxyproject/galaxy/compare/ed4e87ecad31...498dddb03fe3
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: db63b131c1728493a87901764c102dbc47f74f3f
https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c10…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Fix styling, we don't need to force rounded edges here.
Commit: ca24098883fda1c35241d4c380f8b0765de7bb95
https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/style/less/dataset.less
M static/style/blue/base.css
Log Message:
-----------
Remove unused style, we can rely on the :last pseudoclasses for this.
Commit: f8974acba2884dc2fc1728aaa81021708ad05493
https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa810…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Fix styling when only one visualization type exists
Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb
https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes.
Commit: 29cf7187233bbd031f07df4584f1bef55de612e4
https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Minor styling tweaks -- todo: swap from inline to class-based.
Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7
https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/style/blue/base.css
Log Message:
-----------
Standard styles inclusion in .less, more styling to match rounded edges and spacing.
Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8
https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/parse_gx_xsd.py
M doc/patch.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/version.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/workflow_util.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/auth/pam_auth_helper.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/slideshow/build_slideshow.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tools.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/webapps/galaxy/workflow/editor.mako
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
M test/api/test_workflows.py
M test/api/workflows_format_2/main.py
M test/base/api_asserts.py
M test/base/driver_util.py
A test/functional/tools/sam_to_bam.xml
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history
Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3
https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Don't rely on complex, absolute selector, use local element.find()
Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb
https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming /
Commit: d2ab7e701c87f4292b655893103c7842900a47b5
https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/extra-information.js.map
A static/maps/mvc/user/manage-user-information.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
M static/style/blue/base.css
Log Message:
-----------
build the client
Commit: ed4e87ecad31f48ecefa11b7c9a7aae4c71939aa
https://github.com/galaxyproject/galaxy/commit/ed4e87ecad31f48ecefa11b7c9a7…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-15 (Thu, 15 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/extra-information.js.map
A static/maps/mvc/user/manage-user-information.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'release_16.10' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
static/scripts/bundled/login.bundled.js.map
static/style/blue/base.css
Compare: https://github.com/galaxyproject/galaxy/compare/da784093b368...ed4e87ecad31
Branch: refs/heads/release_16.10
Home: https://github.com/galaxyproject/galaxy
Commit: db63b131c1728493a87901764c102dbc47f74f3f
https://github.com/galaxyproject/galaxy/commit/db63b131c1728493a87901764c10…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Fix styling, we don't need to force rounded edges here.
Commit: ca24098883fda1c35241d4c380f8b0765de7bb95
https://github.com/galaxyproject/galaxy/commit/ca24098883fda1c35241d4c380f8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/style/less/dataset.less
M static/style/blue/base.css
Log Message:
-----------
Remove unused style, we can rely on the :last pseudoclasses for this.
Commit: f8974acba2884dc2fc1728aaa81021708ad05493
https://github.com/galaxyproject/galaxy/commit/f8974acba2884dc2fc1728aaa810…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Fix styling when only one visualization type exists
Commit: ce320b66ea1de3c15f4f080f19a729b1ff2087cb
https://github.com/galaxyproject/galaxy/commit/ce320b66ea1de3c15f4f080f19a7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
A bit of refactoring, handling of unavailable tools or tools with no help. Slight style changes.
Commit: 29cf7187233bbd031f07df4584f1bef55de612e4
https://github.com/galaxyproject/galaxy/commit/29cf7187233bbd031f07df4584f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-28 (Mon, 28 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Minor styling tweaks -- todo: swap from inline to class-based.
Commit: 83e1392cf8d875109d121eb9cf13c274659c02b7
https://github.com/galaxyproject/galaxy/commit/83e1392cf8d875109d121eb9cf13…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/style/blue/base.css
Log Message:
-----------
Standard styles inclusion in .less, more styling to match rounded edges and spacing.
Commit: be6a2f8132f3002e0570488a4ad5f80e07b6c2a8
https://github.com/galaxyproject/galaxy/commit/be6a2f8132f3002e0570488a4ad5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-11-29 (Tue, 29 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/parse_gx_xsd.py
M doc/patch.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/data_transfer.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/version.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/translogger.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy_utils/sequence/fastq.py
M lib/galaxy_utils/sequence/vcf.py
M lib/mimeparse.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/workflow_util.py
M scripts/api/data_manager_example_execute.py
M scripts/api/example_watch_folder.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/load_data_with_metadata.py
M scripts/api/repair_tool_shed_repository.py
M scripts/api/reset_metadata_on_installed_repositories.py
M scripts/api/search.py
M scripts/api/sequencer_configuration_create.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/auth/pam_auth_helper.py
M scripts/build_toolbox.py
M scripts/build_universe_config.py
M scripts/check_galaxy.py
M scripts/check_python.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/communication/communication_server.py
M scripts/create_db.py
M scripts/data_libraries/build_lucene_index.py
M scripts/data_libraries/build_whoosh_index.py
M scripts/drmaa_external_killer.py
M scripts/drmaa_external_runner.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/functional_tests.py
M scripts/grt.py
M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_db.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
M scripts/microbes/create_bacteria_table.py
M scripts/microbes/get_builds_lengths.py
M scripts/microbes/harvest_bacteria.py
M scripts/others/incorrect_gops_jobs.py
M scripts/others/incorrect_gops_join_jobs.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/slideshow/build_slideshow.py
M scripts/summarize_timings.py
M scripts/sync_reports_config.py
M scripts/tool_shed/api/add_repository_registry_entry.py
M scripts/tool_shed/api/create_categories.py
M scripts/tool_shed/api/create_users.py
M scripts/tool_shed/api/export.py
M scripts/tool_shed/api/get_filtered_repository_revisions.py
M scripts/tool_shed/api/import_capsule.py
M scripts/tool_shed/api/remove_repository_registry_entry.py
M scripts/tool_shed/api/reset_metadata_on_repositories.py
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/clean_up_tool_dependency_directory.py
M scripts/tool_shed/deprecate_repositories_without_metadata.py
M scripts/tool_shed/migrate_tools_to_repositories.py
M scripts/tool_shed/show_tool_dependency_installation_dir_contents.py
M scripts/tools/maf/check_loc_file.py
M scripts/tools/re_escape_output.py
M scripts/transfer.py
M scripts/update_shed_config_path.py
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tools.js
M static/style/blue/base.css
M static/welcome.html.sample
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
M templates/webapps/galaxy/workflow/editor.mako
A test-data/bam_from_sam.bam
A test-data/sam_with_header.sam
M test/api/test_workflows.py
M test/api/workflows_format_2/main.py
M test/base/api_asserts.py
M test/base/driver_util.py
A test/functional/tools/sam_to_bam.xml
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_command_factory.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tools/data_source/data_source.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into fix_help_history
Commit: 9c435685cded86c36b605bf81eb9bec7f112cce3
https://github.com/galaxyproject/galaxy/commit/9c435685cded86c36b605bf81eb9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-07 (Wed, 07 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
Don't rely on complex, absolute selector, use local element.find()
Commit: 3ab4e1d742fe08701c1b997bf87f8406d1ccdecb
https://github.com/galaxyproject/galaxy/commit/3ab4e1d742fe08701c1b997bf87f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
Log Message:
-----------
The jobs API, which this functionality is based on, requires a logged in user, so prevent anonymous access here. Also shifts to using Galaxy.root correctly, instead of assuming /
Commit: d2ab7e701c87f4292b655893103c7842900a47b5
https://github.com/galaxyproject/galaxy/commit/d2ab7e701c87f4292b655893103c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-12-14 (Wed, 14 Dec 2016)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/style/less/dataset.less
M static/maps/mvc/dataset/dataset-li-edit.js.map
A static/maps/mvc/user/change-password.js.map
A static/maps/mvc/user/extra-information.js.map
A static/maps/mvc/user/manage-user-information.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/dataset/dataset-li-edit.js
A static/scripts/mvc/user/change-password.js
A static/scripts/mvc/user/extra-information.js
A static/scripts/mvc/user/manage-user-information.js
M static/style/blue/base.css
Log Message:
-----------
build the client
Compare: https://github.com/galaxyproject/galaxy/compare/329108f81021...d2ab7e701c87