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[galaxyproject/galaxy] 04a901: [18.01] Fix SQL query for "workflows shared with m...
by GitHub 27 Mar '18
by GitHub 27 Mar '18
27 Mar '18
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55
https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
[18.01] Fix SQL query for "workflows shared with me" as part of workflow index.
Before and after queries here:
https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f
You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user.
Commit: d6be56256fcbee53509dc867d863819621ef1d08
https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d863…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Merge pull request #5782 from jmchilton/fix_1801
[18.01] Fix SQL query for "workflows shared with me" as part of workflow index.
Compare: https://github.com/galaxyproject/galaxy/compare/fbb47f6e03d0...d6be56256fcb
1
0
27 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a4e9fe6834c507137988a1739a3b6a261598ce37
https://github.com/galaxyproject/galaxy/commit/a4e9fe6834c507137988a1739a3b…
Author: Delphine Lariviere <lariviere.delphine(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
A .ci/autopep8.sh
A .ci/check_py3_compatibility.sh
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M .ci/jenkins/api/run_tests.sh
A .ci/jenkins/selenium-compose/Dockerfile
A .ci/jenkins/selenium-compose/docker-compose.yml
A .ci/jenkins/selenium-compose/galaxy.ini
A .ci/jenkins/selenium-compose/run_galaxy.bash
A .ci/jenkins/selenium-compose/run_tests.sh
R .ci/jenkins/selenium/Dockerfile
R .ci/jenkins/selenium/docker-compose.yml
R .ci/jenkins/selenium/galaxy.ini
R .ci/jenkins/selenium/run_galaxy.bash
M .ci/jenkins/selenium/run_tests.sh
R .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CITATION
M CONTRIBUTING.md
M CONTRIBUTORS.md
M Makefile
M README.rst
A SECURITY_POLICY.md
A client/.babelrc
M client/GruntFile.js
M client/README.md
M client/bower.json
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
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A client/galaxy/scripts/mvc/toolshed/workflows-view.js
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M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-select.js
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M client/galaxy/scripts/mvc/ui/ui-tabs.js
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M client/galaxy/scripts/mvc/upload/collection/collection-row.js
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M client/galaxy/scripts/mvc/upload/upload-view.js
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M client/galaxy/scripts/mvc/user/user-preferences.js
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A config/error_report.yml.sample
R config/external_service_types_conf.xml.sample
R config/galaxy.ini.sample
A config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/job_metrics_conf.xml.sample
A config/lmod_modules_mapping.yml.sample
M config/local_conda_mapping.yml.sample
M config/object_store_conf.xml.sample
M config/openid_conf.xml.sample
A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample
A config/plugins/interactive_environments/askomics/config/askomics.ini.sample
A config/plugins/interactive_environments/askomics/config/askomics.xml
A config/plugins/interactive_environments/askomics/static/js/askomics.js
A config/plugins/interactive_environments/askomics/templates/askomics.mako
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/config/neo.xml
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
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/config/charts.xml
R config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/static/client/app.css
R config/plugins/visualizations/charts/static/client/app.js
R config/plugins/visualizations/charts/static/client/components/model.js
R config/plugins/visualizations/charts/static/client/components/screenshot.js
R config/plugins/visualizations/charts/static/client/views/description.js
R config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/groups.js
R config/plugins/visualizations/charts/static/client/views/settings.js
R config/plugins/visualizations/charts/static/client/views/viewer.js
R config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
R config/plugins/visualizations/charts/static/repository/build/others_example.js
R config/plugins/visualizations/charts/static/repository/build/others_example.js.map
R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/registry.js
R config/plugins/visualizations/charts/static/repository/build/registry.js.map
R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
R config/plugins/visualizations/charts/static/repository/registry.json
R config/plugins/visualizations/charts/static/repository/utilities/jobs.js
R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
R config/plugins/visualizations/charts/static/repository/utilities/utils.js
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
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R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
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R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
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R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
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R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
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R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
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R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
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R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/templates/charts.mako
R config/plugins/visualizations/charts/webpack.config.js
A config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/common/templates/script_entry_point.mako
A config/plugins/visualizations/cytoscape/config/cytoscape.xml
A config/plugins/visualizations/cytoscape/package.json
A config/plugins/visualizations/cytoscape/src/script.js
A config/plugins/visualizations/cytoscape/static/logo.png
A config/plugins/visualizations/cytoscape/static/script.js
A config/plugins/visualizations/drawrna/config/drawrna.xml
A config/plugins/visualizations/drawrna/package.json
A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js
A config/plugins/visualizations/drawrna/src/script.js
A config/plugins/visualizations/drawrna/static/logo.png
A config/plugins/visualizations/drawrna/static/script.js
A config/plugins/visualizations/example/config/example.xml
A config/plugins/visualizations/example/package.json
A config/plugins/visualizations/example/src/script.js
A config/plugins/visualizations/example/static/logo.png
A config/plugins/visualizations/example/static/script.js
R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js
R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js
R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png
A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml
A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml
A config/plugins/visualizations/heatmap/heatmap_default/package.json
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A config/plugins/visualizations/scatterplot/.babelrc
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M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
A config/plugins/visualizations/unipept/README.md
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A config/plugins/webhooks/demo/search/config.yml
R config/plugins/webhooks/demo/search/config/searchover.yaml
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R config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/search/styles.css
A config/plugins/webhooks/demo/tool_list/__init__.py
A config/plugins/webhooks/demo/tool_list/config.yml
R config/plugins/webhooks/demo/tool_list/config/tool_list.yml
R config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/__init__.py
A config/plugins/webhooks/demo/tour_generator/config.yml
A config/plugins/webhooks/demo/tour_generator/script.js
A config/plugins/webhooks/demo/tour_generator/styles.css
R config/reports.ini.sample
A config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
A config/user_preferences_extra_conf.yml.sample
A config/workflow_resource_mapper_conf.yml.sample
A config/workflow_resource_params_conf.xml.sample
M config/workflow_schedulers_conf.xml.sample
M contrib/galaxy.debian-init
M contrib/galaxy.fedora-init
M contrib/galaxy_config_merger.py
M contrib/galaxy_supervisor.conf
M contrib/nagios/check_galaxy.py
M create_db.sh
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 cron/updateucsc.sh.sample
M doc/Makefile
R doc/patch.py
M doc/schema_template.md
A doc/source/admin/_inc_proxy_prereq.rst
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M doc/source/lib/galaxy.jobs.metrics.collectl.rst
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M doc/source/lib/galaxy.managers.rst
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M doc/source/slideshow/architecture/galaxy_architecture.md
R external_service_types/454_life_sciences.xml
R external_service_types/applied_biosystems_solid.xml
R external_service_types/pacific_biosciences_smrt_portal.xml
R external_service_types/simple_unknown_sequencer.xml
M extract_dataset_parts.sh
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
A lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
A lib/galaxy/auth/util.py
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/containers/docker_swarm.py
M lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
A lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/chrominfo.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
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M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
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M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
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M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
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_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/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
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/mol_to_smi_converter.xml
A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_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
A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.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.py
A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
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/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.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/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/ngsindex.py
A lib/galaxy/datatypes/phylip.py
A lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/set_metadata_tool.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/test/1.bam
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A lib/galaxy/datatypes/test/454Score.pdf
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
A lib/galaxy/datatypes/test/chebi_57262.v3k.mol
A lib/galaxy/datatypes/test/example.iqtree
A lib/galaxy/datatypes/test/github88.v3k.sdf
A lib/galaxy/datatypes/test/infernal_model.cm
A lib/galaxy/datatypes/test/linkstudies.allegro_fparam
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M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
A lib/galaxy/datatypes/upload_util.py
M lib/galaxy/datatypes/util/generic_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
R lib/galaxy/dependencies/conda-environment.txt
A lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/dependencies/dev-requirements.txt
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A lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
R lib/galaxy/external_services/__init__.py
R lib/galaxy/external_services/actions.py
R lib/galaxy/external_services/parameters.py
R lib/galaxy/external_services/result_handlers/__init__.py
R lib/galaxy/external_services/result_handlers/basic.py
R lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
R lib/galaxy/jobs/deferred/__init__.py
R lib/galaxy/jobs/deferred/data_transfer.py
R lib/galaxy/jobs/deferred/manual_data_transfer.py
R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/mapper.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/collectl/stats.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
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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/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/chronos.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
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M lib/galaxy/jobs/runners/pulsar.py
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M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.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/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/torque.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
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M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/stock_rules.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/api_keys.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
A lib/galaxy/managers/jobs.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
A lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/base.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.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/0009_request_table.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/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
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M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/search_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_dependency_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/util/xml_util.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M manage_db.sh
R manage_tools.sh
R openid/yahoo.xml
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M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/common.py
M scripts/api/copy_hda_to_library_folder.py
M scripts/api/create.py
M scripts/api/data_manager_example_execute.py
M scripts/api/delete.py
M scripts/api/display.py
M scripts/api/example_watch_folder.py
A scripts/api/fetch_to_library.py
A scripts/api/fetch_to_library_example.yml
R scripts/api/form_create_from_xml.py
M scripts/api/history_create_history.py
M scripts/api/history_delete_history.py
M scripts/api/import_library_dataset_to_history.py
M scripts/api/import_workflows_from_installed_tool_shed_repository.py
M scripts/api/install_tool_shed_repositories.py
M scripts/api/library_create_folder.py
M scripts/api/library_create_library.py
M scripts/api/library_upload_dir.py
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R scripts/api/request_type_create_from_xml.py
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R scripts/api/sample_configurations/sample_tracking/request_form.xml
R scripts/api/sample_configurations/sample_tracking/request_type.xml
R scripts/api/sample_configurations/sample_tracking/sample_form.xml
R scripts/api/sample_dataset_update_status.py
R scripts/api/sample_update_state.py
M scripts/api/search.py
R scripts/api/sequencer_configuration_create.py
M scripts/api/update.py
M scripts/api/upload_to_history.py
M scripts/api/workflow_delete.py
M scripts/api/workflow_execute.py
M scripts/api/workflow_execute_parameters.py
M scripts/api/workflow_import.py
M scripts/api/workflow_import_from_file_rpark.py
A scripts/apply_tags.py
R scripts/binary_compatibility.py
M scripts/bootstrap_history.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/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.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
A scripts/common_startup_functions.sh
A scripts/common_startup_variables.sh
M scripts/communication/communication_server.py
M scripts/communication/template/communication.js
A scripts/config_sample_to_kwalify.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
A scripts/dump_library_paths.py
M scripts/dump_tour.py
M scripts/edam_mapping.py
M scripts/external_chown_script.py
M scripts/extract_dataset_part.py
M scripts/extract_toolbox_sections.py
M scripts/fetch_eggs.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/get_platforms.py
A scripts/get_uwsgi_args.py
R scripts/grt.py
R scripts/grt.yml.sample
A scripts/grt/export.py
A scripts/grt/grt.yml.sample
A scripts/grt/upload.py
M scripts/helper.py
M scripts/loc_files/create_all_fasta_loc.py
A scripts/maintenance.sh
M scripts/manage_db.py
M scripts/manage_tool_dependencies.py
R scripts/manage_tools.py
M scripts/metagenomics/convert_title.py
R scripts/microbes/BeautifulSoup.py
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M scripts/others/incorrect_gops_join_jobs.py
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M scripts/sync_reports_config.py
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M setup.cfg
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R static/maps/mvc/workflow/workflow-connector.js.map
R static/maps/mvc/workflow/workflow-forms.js.map
R static/maps/mvc/workflow/workflow-icons.js.map
R static/maps/mvc/workflow/workflow-manager.js.map
R static/maps/mvc/workflow/workflow-node.js.map
R static/maps/mvc/workflow/workflow-terminals.js.map
R static/maps/mvc/workflow/workflow-view-data.js.map
R static/maps/mvc/workflow/workflow-view-node.js.map
R static/maps/mvc/workflow/workflow-view-terminals.js.map
R static/maps/mvc/workflow/workflow-view.js.map
R static/maps/nls/fr/locale.js.map
R static/maps/nls/ja/locale.js.map
R static/maps/nls/locale.js.map
R static/maps/nls/zh/locale.js.map
R static/maps/onload.js.map
R static/maps/polyfills.js.map
R static/maps/reports_webapp/run_stats.js.map
R static/maps/templates/compiled/panel_section.js.map
R static/maps/templates/compiled/tool_form.js.map
R static/maps/templates/compiled/tool_link.js.map
R static/maps/templates/compiled/tool_search.js.map
R static/maps/toolshed.groups.js.map
R static/maps/ui/autocom_tagging.js.map
R static/maps/ui/editable-text.js.map
R static/maps/ui/fa-icon-button.js.map
R static/maps/ui/filter-control.js.map
R static/maps/ui/hoverhighlight.js.map
R static/maps/ui/loading-indicator.js.map
R static/maps/ui/mode-button.js.map
R static/maps/ui/pagination.js.map
R static/maps/ui/peek-column-selector.js.map
R static/maps/ui/popupmenu.js.map
R static/maps/ui/scroll-panel.js.map
R static/maps/ui/search-input.js.map
R static/maps/utils/add-logging.js.map
R static/maps/utils/ajax-queue.js.map
R static/maps/utils/async-save-text.js.map
R static/maps/utils/config.js.map
R static/maps/utils/deferred.js.map
R static/maps/utils/graph.js.map
R static/maps/utils/levenshtein.js.map
R static/maps/utils/localization.js.map
R static/maps/utils/metrics-logger.js.map
R static/maps/utils/natural-sort.js.map
R static/maps/utils/query-string-parsing.js.map
R static/maps/utils/uploadbox.js.map
R static/maps/utils/utils.js.map
R static/maps/viz/bbi-data-manager.js.map
R static/maps/viz/circster.js.map
R static/maps/viz/phyloviz.js.map
R static/maps/viz/sweepster.js.map
R static/maps/viz/trackster.js.map
R static/maps/viz/trackster/filters.js.map
R static/maps/viz/trackster/painters.js.map
R static/maps/viz/trackster/slotting.js.map
R static/maps/viz/trackster/tracks.js.map
R static/maps/viz/trackster/util.js.map
R static/maps/viz/visualization.js.map
R static/maps/viz/viz_views.js.map
R static/scripts/analysis.js
R static/scripts/app.js
R static/scripts/app/analysis.js
R static/scripts/bundled/analysis.bundled.js
R static/scripts/bundled/analysis.bundled.js.map
R static/scripts/bundled/libs.bundled.js
R static/scripts/bundled/libs.bundled.js.map
R static/scripts/bundled/login.bundled.js
R static/scripts/bundled/login.bundled.js.map
R static/scripts/galaxy.interactive_environments.js
R static/scripts/galaxy.js
R static/scripts/galaxy.library.js
R static/scripts/galaxy.menu.js
R static/scripts/galaxy.pages.js
R static/scripts/i18n.js
R static/scripts/layout/generic-nav-view.js
R static/scripts/layout/masthead.js
R static/scripts/layout/menu.js
R static/scripts/layout/modal.js
R static/scripts/layout/page.js
R static/scripts/layout/panel.js
R static/scripts/layout/scratchbook.js
R static/scripts/libs/backbone.js
R static/scripts/libs/bbi/bigwig.js
R static/scripts/libs/bbi/jquery-ajax-native.js
R static/scripts/libs/bbi/jszlib.js
R static/scripts/libs/bbi/spans.js
R static/scripts/libs/bibtex.js
R static/scripts/libs/bootstrap-tour.js
R static/scripts/libs/bootstrap.js
R static/scripts/libs/common-libs.js
R static/scripts/libs/d3.js
R static/scripts/libs/farbtastic.js
R static/scripts/libs/jquery.complexify.js
R static/scripts/libs/jquery.sparklines.js
R static/scripts/libs/jquery/jqtouch.js
R static/scripts/libs/jquery/jquery-ui.js
R static/scripts/libs/jquery/jquery.autocomplete.js
R static/scripts/libs/jquery/jquery.cookie.js
R static/scripts/libs/jquery/jquery.dynatree.js
R static/scripts/libs/jquery/jquery.event.drag.js
R static/scripts/libs/jquery/jquery.event.drop.js
R static/scripts/libs/jquery/jquery.event.hover.js
R static/scripts/libs/jquery/jquery.form.js
R static/scripts/libs/jquery/jquery.js
R static/scripts/libs/jquery/jquery.migrate.js
R static/scripts/libs/jquery/jquery.mousewheel.js
R static/scripts/libs/jquery/jquery.rating.js
R static/scripts/libs/jquery/jquery.wymeditor.js
R static/scripts/libs/jquery/jstorage.js
R static/scripts/libs/jquery/jstree.js
R static/scripts/libs/jquery/select2.js
R static/scripts/libs/raven.js
R static/scripts/libs/require.js
R static/scripts/libs/showdown.js
R static/scripts/libs/toastr.js
R static/scripts/libs/underscore.js
R static/scripts/mvc/annotation.js
R static/scripts/mvc/base-mvc.js
R static/scripts/mvc/base/controlled-fetch-collection.js
R static/scripts/mvc/citation/citation-model.js
R static/scripts/mvc/citation/citation-view.js
R static/scripts/mvc/collection/base-creator.js
R static/scripts/mvc/collection/collection-li-edit.js
R static/scripts/mvc/collection/collection-li.js
R static/scripts/mvc/collection/collection-model.js
R static/scripts/mvc/collection/collection-view-edit.js
R static/scripts/mvc/collection/collection-view.js
R static/scripts/mvc/collection/list-collection-creator.js
R static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R static/scripts/mvc/collection/pair-collection-creator.js
R static/scripts/mvc/dataset/data.js
R static/scripts/mvc/dataset/dataset-choice.js
R static/scripts/mvc/dataset/dataset-li-edit.js
R static/scripts/mvc/dataset/dataset-li.js
R static/scripts/mvc/dataset/dataset-list.js
R static/scripts/mvc/dataset/dataset-model.js
R static/scripts/mvc/dataset/states.js
R static/scripts/mvc/form/form-data.js
R static/scripts/mvc/form/form-input.js
R static/scripts/mvc/form/form-parameters.js
R static/scripts/mvc/form/form-repeat.js
R static/scripts/mvc/form/form-section.js
R static/scripts/mvc/form/form-view.js
R static/scripts/mvc/grid/grid-model.js
R static/scripts/mvc/grid/grid-template.js
R static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/history/copy-dialog.js
R static/scripts/mvc/history/hda-li-edit.js
R static/scripts/mvc/history/hda-li.js
R static/scripts/mvc/history/hda-model.js
R static/scripts/mvc/history/hdca-li-edit.js
R static/scripts/mvc/history/hdca-li.js
R static/scripts/mvc/history/hdca-model.js
R static/scripts/mvc/history/history-content-model.js
R static/scripts/mvc/history/history-contents.js
R static/scripts/mvc/history/history-model.js
R static/scripts/mvc/history/history-preferences.js
R static/scripts/mvc/history/history-structure-view.js
R static/scripts/mvc/history/history-view-annotated.js
R static/scripts/mvc/history/history-view-edit-current.js
R static/scripts/mvc/history/history-view-edit.js
R static/scripts/mvc/history/history-view.js
R static/scripts/mvc/history/job-dag.js
R static/scripts/mvc/history/multi-panel.js
R static/scripts/mvc/history/options-menu.js
R static/scripts/mvc/job/job-li.js
R static/scripts/mvc/job/job-model.js
R static/scripts/mvc/library/library-dataset-view.js
R static/scripts/mvc/library/library-folder-view.js
R static/scripts/mvc/library/library-folderlist-view.js
R static/scripts/mvc/library/library-folderrow-view.js
R static/scripts/mvc/library/library-foldertoolbar-view.js
R static/scripts/mvc/library/library-library-view.js
R static/scripts/mvc/library/library-librarylist-view.js
R static/scripts/mvc/library/library-libraryrow-view.js
R static/scripts/mvc/library/library-librarytoolbar-view.js
R static/scripts/mvc/library/library-model.js
R static/scripts/mvc/list/list-item.js
R static/scripts/mvc/list/list-view.js
R static/scripts/mvc/tag.js
R static/scripts/mvc/tool/tool-form-base.js
R static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form.js
R static/scripts/mvc/tool/tool-template.js
R static/scripts/mvc/tool/tool-webhooks.js
R static/scripts/mvc/tool/tools.js
R static/scripts/mvc/tours.js
R static/scripts/mvc/ui/error-modal.js
R static/scripts/mvc/ui/icon-button.js
R static/scripts/mvc/ui/popup-menu.js
R static/scripts/mvc/ui/ui-buttons.js
R static/scripts/mvc/ui/ui-color-picker.js
R static/scripts/mvc/ui/ui-drilldown.js
R static/scripts/mvc/ui/ui-frames.js
R static/scripts/mvc/ui/ui-list.js
R static/scripts/mvc/ui/ui-misc.js
R static/scripts/mvc/ui/ui-modal.js
R static/scripts/mvc/ui/ui-options.js
R static/scripts/mvc/ui/ui-popover.js
R static/scripts/mvc/ui/ui-portlet.js
R static/scripts/mvc/ui/ui-select-content.js
R static/scripts/mvc/ui/ui-select-default.js
R static/scripts/mvc/ui/ui-select-ftp.js
R static/scripts/mvc/ui/ui-select-library.js
R static/scripts/mvc/ui/ui-select.js
R static/scripts/mvc/ui/ui-slider.js
R static/scripts/mvc/ui/ui-table.js
R static/scripts/mvc/ui/ui-tabs.js
R static/scripts/mvc/ui/ui-thumbnails.js
R static/scripts/mvc/upload/collection/collection-row.js
R static/scripts/mvc/upload/collection/collection-view.js
R static/scripts/mvc/upload/composite/composite-row.js
R static/scripts/mvc/upload/composite/composite-view.js
R static/scripts/mvc/upload/default/default-row.js
R static/scripts/mvc/upload/default/default-view.js
R static/scripts/mvc/upload/upload-button.js
R static/scripts/mvc/upload/upload-ftp.js
R static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-settings.js
R static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/change-password.js
R static/scripts/mvc/user/extra-information.js
R static/scripts/mvc/user/manage-user-information.js
R static/scripts/mvc/user/user-custom-builds.js
R static/scripts/mvc/user/user-model.js
R static/scripts/mvc/user/user-preferences.js
R static/scripts/mvc/user/user-quotameter.js
R static/scripts/mvc/visualization/visualization-model.js
R static/scripts/mvc/webhooks.js
R static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-connector.js
R static/scripts/mvc/workflow/workflow-forms.js
R static/scripts/mvc/workflow/workflow-icons.js
R static/scripts/mvc/workflow/workflow-manager.js
R static/scripts/mvc/workflow/workflow-node.js
R static/scripts/mvc/workflow/workflow-terminals.js
R static/scripts/mvc/workflow/workflow-view-data.js
R static/scripts/mvc/workflow/workflow-view-node.js
R static/scripts/mvc/workflow/workflow-view-terminals.js
R static/scripts/mvc/workflow/workflow-view.js
R static/scripts/nls/fr/locale.js
R static/scripts/nls/ja/locale.js
R static/scripts/nls/locale.js
R static/scripts/nls/zh/locale.js
R static/scripts/onload.js
R static/scripts/packed
R static/scripts/polyfills.js
R static/scripts/reports_webapp/run_stats.js
R static/scripts/ui/autocom_tagging.js
R static/scripts/ui/editable-text.js
R static/scripts/ui/fa-icon-button.js
R static/scripts/ui/filter-control.js
R static/scripts/ui/hoverhighlight.js
R static/scripts/ui/loading-indicator.js
R static/scripts/ui/mode-button.js
R static/scripts/ui/pagination.js
R static/scripts/ui/peek-column-selector.js
R static/scripts/ui/popupmenu.js
R static/scripts/ui/scroll-panel.js
R static/scripts/ui/search-input.js
R static/scripts/utils/add-logging.js
R static/scripts/utils/ajax-queue.js
R static/scripts/utils/async-save-text.js
R static/scripts/utils/config.js
R static/scripts/utils/deferred.js
R static/scripts/utils/graph.js
R static/scripts/utils/levenshtein.js
R static/scripts/utils/localization.js
R static/scripts/utils/metrics-logger.js
R static/scripts/utils/natural-sort.js
R static/scripts/utils/query-string-parsing.js
R static/scripts/utils/uploadbox.js
R static/scripts/utils/utils.js
R static/scripts/viz/bbi-data-manager.js
R static/scripts/viz/circster.js
R static/scripts/viz/phyloviz.js
R static/scripts/viz/sweepster.js
R static/scripts/viz/trackster.js
R static/scripts/viz/trackster/filters.js
R static/scripts/viz/trackster/painters.js
R static/scripts/viz/trackster/slotting.js
R static/scripts/viz/trackster/tracks.js
R static/scripts/viz/trackster/util.js
R static/scripts/viz/visualization.js
R static/scripts/viz/viz_views.js
M static/style/blue/base.css
R static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/trackster.css
M static/toolshed/maps/mvc/groups/group-detail-view.js.map
M static/toolshed/maps/mvc/groups/group-list-view.js.map
M static/toolshed/maps/mvc/groups/group-listrow-view.js.map
M static/toolshed/maps/mvc/groups/group-model.js.map
M static/toolshed/scripts/mvc/groups/group-detail-view.js
M static/toolshed/scripts/mvc/groups/group-list-view.js
M static/toolshed/scripts/mvc/groups/group-listrow-view.js
M static/toolshed/scripts/mvc/groups/group-model.js
M static/welcome.html.sample
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/group/group.mako
R templates/admin/dataset_security/group/group_create.mako
R templates/admin/dataset_security/group/group_rename.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
R templates/admin/external_service/common.mako
R templates/admin/external_service/create_external_service.mako
R templates/admin/external_service/edit_external_service.mako
R templates/admin/external_service/grid.mako
R templates/admin/external_service/reload_external_service_types.mako
R templates/admin/external_service/view_external_service.mako
R templates/admin/forms/create_form.mako
R templates/admin/forms/edit_form_definition.mako
R templates/admin/forms/grid.mako
R templates/admin/forms/view_form_definition.mako
R templates/admin/library/grid.mako
R templates/admin/library/new_library.mako
R templates/admin/package_tool.mako
R templates/admin/quota/grid.mako
R templates/admin/quota/quota.mako
R templates/admin/quota/quota_create.mako
R templates/admin/quota/quota_edit.mako
R templates/admin/quota/quota_rename.mako
R templates/admin/quota/quota_set_default.mako
R templates/admin/reload_tool.mako
R templates/admin/request_type/common.mako
R templates/admin/request_type/create_request_type.mako
R templates/admin/request_type/edit_request_type.mako
R templates/admin/request_type/grid.mako
R templates/admin/request_type/request_type_permissions.mako
R templates/admin/request_type/view_request_type.mako
R templates/admin/requests/grid.mako
R templates/admin/requests/reject.mako
R templates/admin/requests/rename_datasets.mako
R templates/admin/requests/sample_datasets_grid.mako
R templates/admin/requests/view_sample_dataset.mako
R templates/admin/tool_shed_repository/browse_category.mako
R templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
R templates/admin/tool_shed_repository/grid.mako
R templates/admin/tool_shed_repository/initiate_repository_installation.mako
M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
A templates/admin/tool_shed_repository/monitor_repository_installation.mako
R templates/admin/tool_shed_repository/repair_repository.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
R templates/admin/tool_shed_repository/repository_installation_grid.mako
M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
R templates/admin/tool_shed_repository/tool_dependencies_grid.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
R templates/admin/tool_version/grid.mako
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
M templates/base.mako
M templates/base/base_panels.mako
R templates/common/select_template.mako
R templates/common/template_common.mako
M templates/display_base.mako
M templates/display_common.mako
R templates/export_base.mako
R templates/form.mako
M templates/galaxy_client_app.mako
R templates/grid_base.mako
R templates/grid_base_async.mako
M templates/js-app.mako
A templates/legacy/grid_base.mako
A templates/legacy/grid_base_async.mako
R templates/panels.mako
R templates/rss.mako
R templates/search/index.mako
M templates/sharing_base.mako
M templates/show_params.mako
M templates/tagging_common.mako
M templates/user/index.mako
M templates/user/login.mako
M templates/user/logout.mako
M templates/user/openid_manage.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/admin/index.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
R templates/webapps/galaxy/admin/toolsheds.mako
M templates/webapps/galaxy/base_panels.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/dataset/display.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
R templates/webapps/galaxy/dataset/errors.mako
R templates/webapps/galaxy/dataset/grid.mako
M templates/webapps/galaxy/dataset/security_common.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
R templates/webapps/galaxy/external_services/generic_jquery_grid.mako
R templates/webapps/galaxy/external_services/generic_json.mako
R templates/webapps/galaxy/external_services/json_common.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
R templates/webapps/galaxy/history/citations.mako
M templates/webapps/galaxy/history/display.mako
R templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/history/embed.mako
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
R templates/webapps/galaxy/history/list_published.mako
R templates/webapps/galaxy/history/permissions.mako
R templates/webapps/galaxy/history/rename.mako
R templates/webapps/galaxy/history/shared_grid.mako
M templates/webapps/galaxy/history/structure.mako
R templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
R templates/webapps/galaxy/library/common/browse_library.mako
R templates/webapps/galaxy/library/common/browse_library_opt.mako
R templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/library/common/folder_info.mako
R templates/webapps/galaxy/library/common/folder_permissions.mako
R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
R templates/webapps/galaxy/library/common/ldda_edit_info.mako
R templates/webapps/galaxy/library/common/ldda_info.mako
R templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_info.mako
R templates/webapps/galaxy/library/common/library_dataset_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_search_results.mako
R templates/webapps/galaxy/library/common/library_info.mako
R templates/webapps/galaxy/library/common/library_item_info.mako
R templates/webapps/galaxy/library/common/library_permissions.mako
R templates/webapps/galaxy/library/common/move_library_item.mako
R templates/webapps/galaxy/library/common/new_folder.mako
R templates/webapps/galaxy/library/common/upload.mako
R templates/webapps/galaxy/library/grid.mako
R templates/webapps/galaxy/library/index.mako
R templates/webapps/galaxy/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
R templates/webapps/galaxy/mobile/history/detail.mako
R templates/webapps/galaxy/mobile/history/list.mako
R templates/webapps/galaxy/mobile/index.mako
R templates/webapps/galaxy/mobile/manage_library.mako
R templates/webapps/galaxy/mobile/settings.mako
R templates/webapps/galaxy/page/create.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
R templates/webapps/galaxy/page/list_published.mako
R templates/webapps/galaxy/page/select_items_grid.mako
R templates/webapps/galaxy/requests/common/add_samples.mako
R templates/webapps/galaxy/requests/common/common.mako
R templates/webapps/galaxy/requests/common/create_request.mako
R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako
R templates/webapps/galaxy/requests/common/edit_samples.mako
R templates/webapps/galaxy/requests/common/find_samples.mako
R templates/webapps/galaxy/requests/common/index.mako
R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako
R templates/webapps/galaxy/requests/common/sample_datasets.mako
R templates/webapps/galaxy/requests/common/sample_state.mako
R templates/webapps/galaxy/requests/common/view_request.mako
R templates/webapps/galaxy/requests/common/view_request_history.mako
R templates/webapps/galaxy/requests/common/view_sample.mako
R templates/webapps/galaxy/requests/common/view_sample_datasets.mako
R templates/webapps/galaxy/requests/common/view_sample_history.mako
R templates/webapps/galaxy/requests/find_samples_index.mako
R templates/webapps/galaxy/requests/grid.mako
R templates/webapps/galaxy/requests/index.mako
M templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/user/list_users.mako
R templates/webapps/galaxy/visualization/create.mako
M templates/webapps/galaxy/visualization/display.mako
R templates/webapps/galaxy/visualization/list.mako
R templates/webapps/galaxy/visualization/list_published.mako
M templates/webapps/galaxy/visualization/phyloviz.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
R templates/webapps/galaxy/workflow/configure_menu.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/list_for_run.mako
R templates/webapps/galaxy/workflow/list_published.mako
R templates/webapps/galaxy/workflow/run.mako
M templates/webapps/galaxy/workflow/sharing.mako
M templates/webapps/reports/base_panels.mako
R templates/webapps/reports/grid.mako
M templates/webapps/reports/index.mako
R templates/webapps/reports/requests_per_month_all.mako
R templates/webapps/reports/requests_per_user.mako
R templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/admin/center.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/category/grid.mako
M templates/webapps/tool_shed/category/valid_grid.mako
M templates/webapps/tool_shed/common/common.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M templates/webapps/tool_shed/group/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/find_tools.mako
M templates/webapps/tool_shed/repository/find_workflows.mako
R templates/webapps/tool_shed/repository/grid.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/repository_review/browse_review.mako
M templates/webapps/tool_shed/repository_review/edit_review.mako
M templates/webapps/tool_shed/repository_review/grid.mako
M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako
M templates/webapps/tool_shed/user/manage_email_alerts.mako
A test-data/1.csv
M test-data/1.fastqsanger
M test-data/1.fastqsolexa
A test-data/1.sam.gz
A test-data/5_Ig-like.gff
A test-data/bad.html.gz
A test-data/bam_native_from_sam.bam
A test-data/example-bag.zip
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
M test-data/neostore.zip
A test-data/new_element_sort_order.txt
A test-data/new_tags_1.txt
A test-data/qname_sorted.bam
A test-data/random-file
M test-data/sam_with_header.sam
A test-data/selenium-test-notebook.ipynb
M test-data/simple_line_alternative.txt
M test-data/simple_lines_interleaved.txt
A test-data/test.vcf.gz
A test-data/testdir1.zip
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_configuration.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_framework.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_search.py
M test/api/test_tool_data.py
M test/api/test_tools.py
A test/api/test_tools_upload.py
M test/api/test_tours.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_webhooks.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/api_util.py
A test/base/constants.py
M test/base/data/test_workflow_1.ga
M test/base/driver_util.py
M test/base/instrument.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/populators.py
R test/base/test_db_util.py
A test/base/testcase.py
R test/base/tool_shed_util.py
R test/base/twilltestcase.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
R test/casperjs/README.txt
R test/casperjs/api-anon-history-permission-tests.js
R test/casperjs/api-anon-history-tests.js
R test/casperjs/api-hda-tests.js
R test/casperjs/api-history-permission-tests.js
R test/casperjs/casperjs_runner.py
R test/casperjs/modules/api.js
R test/casperjs/modules/historyoptions.js
R test/casperjs/modules/historypanel.js
R test/casperjs/modules/tools.js
R test/casperjs/modules/user.js
R test/casperjs/page-data/selectors.json
R test/casperjs/server_env.py
R test/casperjs/spaceghost.js
R test/casperjs/test-data/simple_test.ga
R test/casperjs/utils/simple-galaxy.js
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
A test/docker/base/selenium/LICENSE
A test/docker/base/selenium/README
A test/docker/base/selenium/entry_point.sh
A test/docker/base/selenium/functions.sh
A test/docker/base/selenium/generate_config
A test/docker/base/selenium/wrap_chrome_binary
R test/functional/database_contexts.py
M test/functional/test_data_managers.py
R test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/bibtex.xml
A test/functional/tools/cat_data_and_sleep.xml
M test/functional/tools/code_file.py
M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
M test/functional/tools/collection_creates_dynamic_nested.xml
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/collection_split_on_column.xml
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
A test/functional/tools/compressed_neostorezip_neostore_conversion.xml
A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml
A test/functional/tools/config_vars.xml
M test/functional/tools/create_2.xml
A test/functional/tools/data_source.py
A test/functional/tools/empty_datasets.xml
A test/functional/tools/exit_code_oom.xml
A test/functional/tools/fail_identifier.xml
A test/functional/tools/fail_writing_work_dir_file.xml
A test/functional/tools/for_workflows/count_list.xml
A test/functional/tools/for_workflows/count_multi_file.xml
A test/functional/tools/for_workflows/empty_list.xml
A test/functional/tools/identifier_in_actions.xml
A test/functional/tools/identifier_source.xml
A test/functional/tools/job_environment_default.xml
A test/functional/tools/job_environment_default_legacy.xml
A test/functional/tools/job_environment_explicit_shared_home.xml
M test/functional/tools/job_properties.xml
M test/functional/tools/metadata.xml
A test/functional/tools/mulled_example_explicit.xml
A test/functional/tools/mulled_example_multi_versionless.xml
A test/functional/tools/mulled_example_simple.xml
A test/functional/tools/multi_output_recurse.xml
A test/functional/tools/output_filter_with_input.xml
A test/functional/tools/sam_to_unsorted_bam.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/test_data_source.xml
M test/functional/tools/tool_provided_metadata_1.xml
M test/functional/tools/tool_provided_metadata_2.xml
M test/functional/tools/tool_provided_metadata_3.xml
A test/functional/tools/tool_provided_metadata_4.xml
A test/functional/tools/tool_provided_metadata_5.xml
A test/functional/tools/tool_provided_metadata_6.xml
A test/functional/tools/tool_provided_metadata_7.xml
A test/functional/tools/tool_provided_metadata_8.xml
A test/functional/tools/tool_provided_metadata_9.xml
A test/functional/tools/vcf_bgzip.xml
A test/functional/twilltestcase.py
A test/functional/webhooks/history_test1/config.yml
R test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config.yml
R test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config.yml
R test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/__init__.py
A test/functional/webhooks/phdcomics/config.yaml
R test/functional/webhooks/phdcomics/config/phdcomics.yaml
R test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/script.js
R test/functional/webhooks/phdcomics/static/script.js
R test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/phdcomics/styles.css
A test/functional/webhooks/tour_generator
A test/functional/webhooks/trans_object/__init__.py
A test/functional/webhooks/trans_object/config.yaml
R test/functional/webhooks/trans_object/config/trans_object.yaml
R test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config.yml
R test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/script.js
R test/functional/webhooks/xkcd/static/script.js
R test/functional/webhooks/xkcd/static/styles.css
A test/functional/webhooks/xkcd/styles.css
A test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
A test/galaxy_selenium/navigation.yml
M test/galaxy_selenium/sizzle.py
A test/galaxy_selenium/smart_components.py
A test/integration/dockerized_job_conf.xml
A test/integration/resubmission_dynamic_job_conf.xml
M test/integration/resubmission_rules/rules.py
A test/integration/resubmission_small_memory_job_conf.xml
A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml
A test/integration/sets_tmp_dir_expression_job_conf.xml
A test/integration/sets_tmp_dir_to_true_job_conf.xml
A test/integration/simple_job_conf.xml
A test/integration/test_config_options_users.py
A test/integration/test_data_manager_table_reload.py
A test/integration/test_dockerized_jobs.py
A test/integration/test_job_environments.py
M test/integration/test_job_resubmission.py
A test/integration/test_local_job_cancellation.py
R test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_mules_as_job_handlers.py
M test/integration/test_resolvers.py
A test/integration/test_shed_tool_tests.py
A test/integration/test_upload_configuration_options.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/test_workflow_scheduling_options.py
A test/integration/tool_sheds_conf.xml
A test/integration/uses_shed.py
M test/manual/launch_and_run.sh
M test/manual/workflows_scaling.py
R test/qunit/Gruntfile.js
R test/qunit/README.txt
R test/qunit/package.json
R test/qunit/scripts
R test/qunit/test-app.js
R test/qunit/test-common.js
R test/qunit/test-data/bootstrapped.js
R test/qunit/test-data/fakeserver.js
R test/qunit/test-data/job-dag-1.js
R test/qunit/test-data/paired-collection-creator.data.js
R test/qunit/test-libs/qunit-1.23.1.css
R test/qunit/test-libs/qunit-1.23.1.js
R test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-qunit-1.0.0.js
R test/qunit/tests/form_tests.html
R test/qunit/tests/form_tests.js
R test/qunit/tests/galaxy-app-base.html
R test/qunit/tests/galaxy-app-base.js
R test/qunit/tests/graph.html
R test/qunit/tests/graph.js
R test/qunit/tests/hda-base.html
R test/qunit/tests/hda-base.js
R test/qunit/tests/history_contents_model_tests.html
R test/qunit/tests/history_contents_model_tests.js
R test/qunit/tests/job-dag.html
R test/qunit/tests/job-dag.js
R test/qunit/tests/list-of-pairs-collection-creator.html
R test/qunit/tests/list-of-pairs-collection-creator.js
R test/qunit/tests/masthead_tests.html
R test/qunit/tests/masthead_tests.js
R test/qunit/tests/metrics-logger.html
R test/qunit/tests/metrics-logger.js
R test/qunit/tests/modal_tests.html
R test/qunit/tests/modal_tests.js
R test/qunit/tests/page_tests.html
R test/qunit/tests/page_tests.js
R test/qunit/tests/popover_tests.html
R test/qunit/tests/popover_tests.js
R test/qunit/tests/ui_tests.html
R test/qunit/tests/ui_tests.js
R test/qunit/tests/upload_dialog_tests.html
R test/qunit/tests/upload_dialog_tests.js
R test/qunit/tests/utils_test.html
R test/qunit/tests/utils_test.js
R test/qunit/tests/workflow_editor_tests.html
R test/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Merge pull request #1 from galaxyproject/dev
Update from Galaxyproject repo
Commit: ed86fe745f53b151dce03cf571f306d293e59ab9
https://github.com/galaxyproject/galaxy/commit/ed86fe745f53b151dce03cf571f3…
Author: Delphine-L <lariviere.delphine(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml
A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
add genbank.gz andgbk.gz datatypes
Commit: 1e7c86323258676938a060077fca8ad8a41d43e4
https://github.com/galaxyproject/galaxy/commit/1e7c86323258676938a060077fca…
Author: Delphine-L <lariviere.delphine(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
addition of blank lines (test failures)
Commit: e0b9e93b4b76e4e9d553e61f2faa71d6bf559981
https://github.com/galaxyproject/galaxy/commit/e0b9e93b4b76e4e9d553e61f2faa…
Author: Delphine-L <lariviere.delphine(a)gmail.com>
Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths:
M config/datatypes_conf.xml.sample
R lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml
M lib/galaxy/datatypes/sequence.py
Log Message:
-----------
removed gbk.gz extension
Commit: a97b3a469c83f8f6780fd0b84f70ea31e08b6f91
https://github.com/galaxyproject/galaxy/commit/a97b3a469c83f8f6780fd0b84f70…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.genbank
A lib/galaxy/datatypes/test/1.genbank.gz
M tox.ini
Log Message:
-----------
fex sniffing of compressed genbank files
also add doctest for both compressed and uncompressed versions
Commit: 2558d278010999b96aaf279c4eaf539614844de7
https://github.com/galaxyproject/galaxy/commit/2558d278010999b96aaf279c4eaf…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml
M lib/galaxy/datatypes/sequence.py
A lib/galaxy/datatypes/test/1.genbank
A lib/galaxy/datatypes/test/1.genbank.gz
M tox.ini
Log Message:
-----------
Merge pull request #5772 from Delphine-L/addGbkgz
Add genbank.gz datatype
Compare: https://github.com/galaxyproject/galaxy/compare/c5beedef6b9f...2558d2780109
1
0
[galaxyproject/galaxy] 571fed: Remove menu options from visualization tab, shift ...
by GitHub 27 Mar '18
by GitHub 27 Mar '18
27 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 571fedf00654c36ee60115abff50d4d4d4031a5b
https://github.com/galaxyproject/galaxy/commit/571fedf00654c36ee60115abff50…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-02-28 (Wed, 28 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/style/blue/base.css
Log Message:
-----------
Remove menu options from visualization tab, shift tab to workflows
Commit: 0bd98c320ee0ca8c998dfbfc8f84a174066969a7
https://github.com/galaxyproject/galaxy/commit/0bd98c320ee0ca8c998dfbfc8f84…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-02-28 (Wed, 28 Feb 2018)
Changed paths:
A lib/galaxy/webapps/galaxy/api/plugins.py
Log Message:
-----------
Add plugins endpoint
Commit: cc3e5244d603e13afcf4501aefc88868e971fe50
https://github.com/galaxyproject/galaxy/commit/cc3e5244d603e13afcf4501aefc8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-02-28 (Wed, 28 Feb 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/plugins.py
Log Message:
-----------
Remove unused imports from plugins api endpoint
Commit: 1ca6499ea10c35d1647898d50dfac442055fa1cc
https://github.com/galaxyproject/galaxy/commit/1ca6499ea10c35d1647898d50dfa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-02-28 (Wed, 28 Feb 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/components/PluginList.vue
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add vue list for plugins
Commit: f4e52caab6027a50b631331ad3cd02fd3ca2a0a8
https://github.com/galaxyproject/galaxy/commit/f4e52caab6027a50b631331ad3cd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-02-28 (Wed, 28 Feb 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Remove id from header value
Commit: 82e58d9086e7e0da86aab270d07bf8ff442cb2e4
https://github.com/galaxyproject/galaxy/commit/82e58d9086e7e0da86aab270d07b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-02-28 (Wed, 28 Feb 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Redirect to list of plugins
Commit: fbead2daa5ea1da1974ed60e3740a2530165996c
https://github.com/galaxyproject/galaxy/commit/fbead2daa5ea1da1974ed60e3740…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
Log Message:
-----------
Add select field to thumbnail view to allow dataset selection
Commit: d5d60e95aa749c6f14dbc9ae01dcf3e515ce0c2f
https://github.com/galaxyproject/galaxy/commit/d5d60e95aa749c6f14dbc9ae01dc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
M lib/galaxy/visualization/plugins/plugin.py
Log Message:
-----------
Remove comment and debug output
Commit: 15636fa6f144f4a2203b76df0b47cd7d70d03ada
https://github.com/galaxyproject/galaxy/commit/15636fa6f144f4a2203b76df0b47…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/plugins.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Revise resource mapping, add show action to plugins endpoint
Commit: a8daf446eab87cffb5483a6d96b5f8d244d8286c
https://github.com/galaxyproject/galaxy/commit/a8daf446eab87cffb5483a6d96b5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
M lib/galaxy/webapps/galaxy/api/plugins.py
Log Message:
-----------
Add error handlers, populate select list with applicable datasets
Commit: b6ad62c0e09d3c67951849cdaeb340e9bc9f11a0
https://github.com/galaxyproject/galaxy/commit/b6ad62c0e09d3c67951849cdaeb3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Add event handler for create button
Commit: a1f9cdcf45ccb448341d60f5eed6e32303244a39
https://github.com/galaxyproject/galaxy/commit/a1f9cdcf45ccb448341d60f5eed6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Restore sub menu options for visualization tab
Commit: 8763a2c25fb0237e1dc23b06845e249ca1bc687a
https://github.com/galaxyproject/galaxy/commit/8763a2c25fb0237e1dc23b06845e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Add simple filter search
Commit: 923286612d7e31ffaf474a60392960f36345895f
https://github.com/galaxyproject/galaxy/commit/923286612d7e31ffaf474a603929…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Revise dataset selection label
Commit: a077f45ba9830136f2869e39e50680e7dfc41c5b
https://github.com/galaxyproject/galaxy/commit/a077f45ba9830136f2869e39e506…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Match search word with description
Commit: 980f2b9708cb9e95bbacf0ae0decb42f7cd0da6c
https://github.com/galaxyproject/galaxy/commit/980f2b9708cb9e95bbacf0ae0dec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M config/plugins/visualizations/scatterplot/package.json
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.js
Log Message:
-----------
Partial fix for internal scatterplot
Commit: a6559248c9e877911ed86b08135f7aae6408fb0b
https://github.com/galaxyproject/galaxy/commit/a6559248c9e877911ed86b08135f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M config/plugins/visualizations/scatterplot/src/scatterplot.js
Log Message:
-----------
Remove comments
Commit: 044ca897d53c08939508935c003c5e3d665ba769
https://github.com/galaxyproject/galaxy/commit/044ca897d53c08939508935c003c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
Log Message:
-----------
Add confirm option
Commit: 58f0afe23b9c9590bd8cda1dd4d7c3b731fb0969
https://github.com/galaxyproject/galaxy/commit/58f0afe23b9c9590bd8cda1dd4d7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Hide grid if error occurs
Commit: eec8bf47036c0057f9a21578159199b6c036acbb
https://github.com/galaxyproject/galaxy/commit/eec8bf47036c0057f9a215781591…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
Log Message:
-----------
Augment button model with visibile attribute
Commit: 7f342c340e7739854a1cd7fda375d947aa8addb2
https://github.com/galaxyproject/galaxy/commit/7f342c340e7739854a1cd7fda375…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/style/less/charts.less
M static/style/blue/base.css
Log Message:
-----------
Fix default inline handler, fix fullscreen switch
Commit: 4f4c8967c0de717f27b5057aaeaef8e3b4d0da98
https://github.com/galaxyproject/galaxy/commit/4f4c8967c0de717f27b5057aaeae…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
M client/galaxy/scripts/mvc/visualization/chart/views/groups.js
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml
M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml
M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
Log Message:
-----------
Fix modified handler
Commit: f47b88730b2dba31daeeba76f76b06aea44fdbc6
https://github.com/galaxyproject/galaxy/commit/f47b88730b2dba31daeeba76f76b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
Log Message:
-----------
Remove unused variable
Commit: bebc022d6f6c6a0dff627381c7c435fffbdbe3e0
https://github.com/galaxyproject/galaxy/commit/bebc022d6f6c6a0dff627381c7c4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
Log Message:
-----------
Add info notification for visualizations which require additional confirmation
Commit: 5e98958c22dba2665f762052e4d017145a243395
https://github.com/galaxyproject/galaxy/commit/5e98958c22dba2665f762052e4d0…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
M client/galaxy/style/less/charts.less
M static/style/blue/base.css
Log Message:
-----------
Highlight check button to confirm settings
Commit: eadeb0f91717e24464279b4d694bf0725710048b
https://github.com/galaxyproject/galaxy/commit/eadeb0f91717e24464279b4d694b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
M config/plugins/visualizations/venn/src/script.js
M config/plugins/visualizations/venn/static/script.js
Log Message:
-----------
Add additional data validation
Commit: e01d1a0049ebc2ca7c05b0439d461afa9a38ea70
https://github.com/galaxyproject/galaxy/commit/e01d1a0049ebc2ca7c05b0439d46…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js
M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
Log Message:
-----------
Fix data validation for pie charts
Commit: 88be6acf911333f1a54d7eef6b564971150cbdff
https://github.com/galaxyproject/galaxy/commit/88be6acf911333f1a54d7eef6b56…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-06 (Tue, 06 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/extended.js
A client/galaxy/scripts/components/DisplayStructured.vue
A client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-list.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/list/list-view.js
M client/galaxy/scripts/mvc/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/utils/utils.js
M config/datatypes_conf.xml.sample
M lib/galaxy/actions/library.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.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/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/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_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/sam_to_bam_native.xml
A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/containers.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cwl/util.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/containers.py
M 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/lmod.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/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
A lib/galaxy/util/create_history_template.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/monitors.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
M scripts/migrate_tools/migrate_tools.py
R templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/view.mako
A test-data/qname_sorted.bam
M test/functional/tools/multi_output_recurse.xml
M test/functional/tools/sam_to_bam_native.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/unit/tools/test_toolbox.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: 04bfefb7dae2a0d035d76f57a6c552facee8bd19
https://github.com/galaxyproject/galaxy/commit/04bfefb7dae2a0d035d76f57a6c5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-08 (Thu, 08 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/style/less/ui.less
M config/galaxy.yml.sample
M config/plugins/webhooks/demo/tour_generator/__init__.py
M doc/source/admin/galaxy_options.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/managers/workflows.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/test.py
M lib/galaxy/tools/verify/asserts/__init__.py
A lib/galaxy/tools/verify/interactor.py
A lib/galaxy/tools/verify/script.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/validation.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/tool_shed/util/workflow_util.py
R scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M static/style/blue/base.css
M test/api/test_tools.py
M test/base/api.py
M test/base/driver_util.py
M test/base/interactor.py
M test/base/testcase.py
R test/base/tool_shed_util.py
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
M test/functional/twilltestcase.py
M test/integration/test_data_manager_table_reload.py
A test/integration/test_shed_tool_tests.py
A test/integration/uses_shed.py
M test/shed_functional/base/twilltestcase.py
M test/unit/tools/test_parsing.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: e57136523c5e5674c1091cfcec601a5b65fc3fd3
https://github.com/galaxyproject/galaxy/commit/e57136523c5e5674c1091cfcec60…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-08 (Thu, 08 Mar 2018)
Changed paths:
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
Log Message:
-----------
Fix trackster urls
Commit: 840ad914c5a3ce7ad7b8fd2f4c4f5bf051543c95
https://github.com/galaxyproject/galaxy/commit/840ad914c5a3ce7ad7b8fd2f4c4f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-08 (Thu, 08 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Move url creation to plugins
Commit: f3eb82208971e151399ac2c7d7539d7d8ca1630b
https://github.com/galaxyproject/galaxy/commit/f3eb82208971e151399ac2c7d753…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
Log Message:
-----------
Revise url generator
Commit: 4c49af552787bcf89e363323dc6eda5dfb12d8cf
https://github.com/galaxyproject/galaxy/commit/4c49af552787bcf89e363323dc6e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/visualization-view.js
Log Message:
-----------
Client parses url parameters
Commit: b42960951af3b438050751f208c5452421f60a80
https://github.com/galaxyproject/galaxy/commit/b42960951af3b438050751f208c5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
Log Message:
-----------
Restore built-in location
Commit: b35a4dfe017b43b49400090e662c9eebb8e62dfa
https://github.com/galaxyproject/galaxy/commit/b35a4dfe017b43b49400090e662c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M config/plugins/visualizations/csg/config/csg.xml
A config/plugins/visualizations/csg/static/logo.png
M config/plugins/visualizations/phyloviz/config/phyloviz.xml
A config/plugins/visualizations/phyloviz/static/logo.png
M config/plugins/visualizations/trackster/config/trackster.xml
A config/plugins/visualizations/trackster/static/logo.png
Log Message:
-----------
Add description for trackster and other visualizations
Commit: dc3cd003549cd9f54e7a955af8e7ecec355c2a44
https://github.com/galaxyproject/galaxy/commit/dc3cd003549cd9f54e7a955af8e7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/unipept/config/unipept.xml
Log Message:
-----------
Add additional descriptions
Commit: ace94178c8af8cbd8d098229d96a7a27104da798
https://github.com/galaxyproject/galaxy/commit/ace94178c8af8cbd8d098229d96a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
Log Message:
-----------
Revise data submission tool
Commit: 553474ddfd32229787630989099127e8029dd4f9
https://github.com/galaxyproject/galaxy/commit/553474ddfd322297876309890991…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M config/plugins/visualizations/example/config/example.xml
Log Message:
-----------
Hide example plugin
Commit: f08223bc7a7ac7e9827543601707009c2ac8a0f1
https://github.com/galaxyproject/galaxy/commit/f08223bc7a7ac7e9827543601707…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M lib/galaxy/visualization/plugins/registry.py
Log Message:
-----------
Sort plugins by display name
Commit: 7d95d28d7c729ff25fe8f9f21e9bd7fcad183cbe
https://github.com/galaxyproject/galaxy/commit/7d95d28d7c729ff25fe8f9f21e9b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M config/plugins/visualizations/trackster/config/trackster.xml
Log Message:
-----------
Increase priority for trackster
Commit: e0c25f42668f3956ee152843057fda74cdea79a4
https://github.com/galaxyproject/galaxy/commit/e0c25f42668f3956ee152843057f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M config/plugins/visualizations/example/config/example.xml
Log Message:
-----------
Enable example
Commit: 1aa5f8283eaaf5f03b929215ffd49982a74febc2
https://github.com/galaxyproject/galaxy/commit/1aa5f8283eaaf5f03b929215ffd4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M lib/galaxy/visualization/plugins/registry.py
Log Message:
-----------
Fix lint
Commit: 7afecf9d1ab0b5d6ad5c34a180ff599b318bc0a1
https://github.com/galaxyproject/galaxy/commit/7afecf9d1ab0b5d6ad5c34a180ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
Log Message:
-----------
Fix test cases
Commit: 00f282ccaab220d290a298f28fe8d9b113cf908b
https://github.com/galaxyproject/galaxy/commit/00f282ccaab220d290a298f28fe8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/webapps/galaxy/api/plugins.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Use vue instead of backbone view
Commit: cb9ecb63f533dfc648af1b016975f89cb2591bfe
https://github.com/galaxyproject/galaxy/commit/cb9ecb63f533dfc648af1b016975…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
R client/galaxy/scripts/mvc/visualization/visualization-view.js
Log Message:
-----------
Remove backbone visualization selector
Commit: b325e086f20f241bc2c2a39a705b7d12bda5e06d
https://github.com/galaxyproject/galaxy/commit/b325e086f20f241bc2c2a39a705b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
Log Message:
-----------
Remove unused import
Commit: 9f52c391229d07687dfa792fa525cb8c781e3b93
https://github.com/galaxyproject/galaxy/commit/9f52c391229d07687dfa792fa525…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Use parsed dataset id in visualization selector instead of showing select field
Commit: 21aa7462875f064766be2e5a6e7b35f7de7dc2b0
https://github.com/galaxyproject/galaxy/commit/21aa7462875f064766be2e5a6e7b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Fix button inline style
Commit: c14ed8732f76cab4e72371878fd770fc01c7bfb0
https://github.com/galaxyproject/galaxy/commit/c14ed8732f76cab4e72371878fd7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Temporary use of style section in vue component
Commit: 9bb1e48aba4bd5de3d0b59b113d8dce2d047612b
https://github.com/galaxyproject/galaxy/commit/9bb1e48aba4bd5de3d0b59b113d8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-09 (Fri, 09 Mar 2018)
Changed paths:
M config/job_metrics_conf.xml.sample
M lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/upload_util.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/__init__.py
A lib/galaxy/jobs/metrics/instrumenters/cgroup.py
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/tools/data_fetch.py
A lib/galaxy/tools/data_fetch.xml
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/special_tools.py
M lib/galaxy/util/compression_utils.py
A lib/galaxy/webapps/galaxy/api/_fetch_util.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
A scripts/api/fetch_to_library.py
A scripts/api/fetch_to_library_example.yml
A test-data/1.csv
A test-data/example-bag.zip
A test-data/testdir1.zip
M test/api/test_dataset_collections.py
M test/api/test_libraries.py
M test/api/test_tools_upload.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
M test/integration/test_upload_configuration_options.py
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: a706929bd6fe7f9d502e756cc592806a79480147
https://github.com/galaxyproject/galaxy/commit/a706929bd6fe7f9d502e756cc592…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-12 (Mon, 12 Mar 2018)
Changed paths:
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/filters.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/slotting.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M config/datatypes_conf.xml.sample
A doc/source/releases/18.01.rst
M doc/source/releases/18.01_announce.rst
A doc/source/releases/18.05_announce.rst
M doc/source/releases/index.rst
M lib/galaxy/containers/docker_model.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
R lib/galaxy/datatypes/converters/sam_to_bam_native.xml
A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
M lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
M lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/verify/script.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/tool_shed/util/tool_util.py
M test/functional/test_toolbox.py
R test/functional/tools/sam_to_bam_native.xml
A test/functional/tools/sam_to_unsorted_bam.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: ef619f5905820d635f068a5c372b4167dec121bd
https://github.com/galaxyproject/galaxy/commit/ef619f5905820d635f068a5c372b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M doc/source/releases/18.01_announce.rst
M lib/galaxy/managers/libraries.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/workflow/run_request.py
M scripts/common_startup.sh
M test/api/test_workflows.py
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: c07c17e93dbd137947320b417082733a8a34345e
https://github.com/galaxyproject/galaxy/commit/c07c17e93dbd137947320b417082…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M config/plugins/visualizations/msa/static/script.js
Log Message:
-----------
Restore missing src for msa
Commit: f58507880e26693a3142c94023e1f010e668b126
https://github.com/galaxyproject/galaxy/commit/f58507880e26693a3142c94023e1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-13 (Tue, 13 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/form/form-data.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/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: bf30a02f1e03f6058c755489a9aa1503463cf8c3
https://github.com/galaxyproject/galaxy/commit/bf30a02f1e03f6058c755489a9aa…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-14 (Wed, 14 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.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-view.js
M client/galaxy/scripts/utils/uploadbox.js
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/web/framework/decorators.py
A lib/galaxy/webapps/galaxy/api/uploads.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/root.py
M test/base/driver_util.py
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: df5838e6c1924e2f0303c675e0262736ece52238
https://github.com/galaxyproject/galaxy/commit/df5838e6c1924e2f0303c675e026…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-14 (Wed, 14 Mar 2018)
Changed paths:
M client/galaxy/scripts/viz/trackster.js
Log Message:
-----------
Fix trackster link
Commit: 7c3c36e7626769c653b9b3b8f6208c861c60a24d
https://github.com/galaxyproject/galaxy/commit/7c3c36e7626769c653b9b3b8f620…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
A config/plugins/visualizations/scatterplot/static/logo.png
Log Message:
-----------
Add logo for scatterplot
Commit: 0e150b4051b9ff567e5c5a26fb213d36d42ebdf9
https://github.com/galaxyproject/galaxy/commit/0e150b4051b9ff567e5c5a26fb21…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M client/galaxy/scripts/layout/menu.js
Log Message:
-----------
Rename tab to Visualize
Commit: e0572e104fb4589c58415bb3d5f99ffe996b2f9c
https://github.com/galaxyproject/galaxy/commit/e0572e104fb4589c58415bb3d5f9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M Makefile
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.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/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/package.json
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
A config/plugins/visualizations/scatterplot/.babelrc
M config/plugins/visualizations/scatterplot/package.json
A config/plugins/visualizations/scatterplot/src/jqglobals.js
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_shed.yml.sample
A config/workflow_resource_mapper_conf.yml.sample
A config/workflow_resource_params_conf.xml.sample
M doc/source/admin/cluster.md
M doc/source/admin/nginx.md
M doc/source/admin/scaling.md
M doc/source/releases/18.01_announce.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data_fetch.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/_fetch_util.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/modules.py
A lib/galaxy/workflow/resources/__init__.py
A lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run_request.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M run_tests.sh
A scripts/apply_tags.py
M scripts/bootstrap_history.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M test/api/test_libraries.py
M test/api/test_tools_upload.py
M test/api/test_workflows.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
M test/integration/test_upload_configuration_options.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_to_collections.py
M test/selenium_tests/test_tool_form.py
M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml
M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/dynamic_tool_destination/ymltests.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into visualization_header
Commit: 8b5c0b223ef9092420b9912b153b0d257fe5a1a5
https://github.com/galaxyproject/galaxy/commit/8b5c0b223ef9092420b9912b153b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M client/galaxy/scripts/components/PluginList.vue
Log Message:
-----------
Allow target top rendering for visualizations
Commit: 0cdd9b9ecd235a34ba6018542156f9780bf22f77
https://github.com/galaxyproject/galaxy/commit/0cdd9b9ecd235a34ba6018542156…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
Log Message:
-----------
Client formatting
Commit: 2b2fd9289857b258f7e63f64668d776c49a54ec8
https://github.com/galaxyproject/galaxy/commit/2b2fd9289857b258f7e63f64668d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Use visualizations route to link to plugins
Commit: 38c2a895009c03204026ca7d74af70f92dd29f4e
https://github.com/galaxyproject/galaxy/commit/38c2a895009c03204026ca7d74af…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge branch 'visualization_header' of github.com:guerler/galaxy into visualization_header
Commit: c5beedef6b9f4498e4df0adfb39ddc519715f997
https://github.com/galaxyproject/galaxy/commit/c5beedef6b9f4498e4df0adfb39d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/components/HistoryImport.vue
A client/galaxy/scripts/components/PluginList.vue
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
M client/galaxy/scripts/mvc/visualization/chart/views/groups.js
M client/galaxy/scripts/mvc/visualization/chart/views/menu.js
M client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
R client/galaxy/scripts/mvc/visualization/visualization-view.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/charts.less
M config/plugins/visualizations/csg/config/csg.xml
A config/plugins/visualizations/csg/static/logo.png
M config/plugins/visualizations/graphviz/config/graphviz.xml
M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml
M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml
M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
M config/plugins/visualizations/msa/static/script.js
M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js
M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
M config/plugins/visualizations/phyloviz/config/phyloviz.xml
A config/plugins/visualizations/phyloviz/static/logo.png
M config/plugins/visualizations/scatterplot/src/scatterplot.js
A config/plugins/visualizations/scatterplot/static/logo.png
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/trackster/config/trackster.xml
A config/plugins/visualizations/trackster/static/logo.png
M config/plugins/visualizations/unipept/config/unipept.xml
M config/plugins/visualizations/venn/src/script.js
M config/plugins/visualizations/venn/static/script.js
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
A lib/galaxy/webapps/galaxy/api/plugins.py
M lib/galaxy/webapps/galaxy/buildapp.py
M static/style/blue/base.css
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
Log Message:
-----------
Merge branch 'visualization_header' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/bf5d472e2850...c5beedef6b9f
1
0
[galaxyproject/usegalaxy-playbook] 6f9370: Upgraded dunovo on test and main, upgraded extract...
by GitHub 27 Mar '18
by GitHub 27 Mar '18
27 Mar '18
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 6f9370135835b80ee1a1ec77d0133ae4aec364bf
https://github.com/galaxyproject/usegalaxy-playbook/commit/6f9370135835b80e…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M env/main/files/galaxy/var/integrated_tool_panel.xml
M env/main/files/galaxy/var/shed_tool_conf.xml
M env/test/files/galaxy/var/integrated_tool_panel.xml
M env/test/files/galaxy/var/shed_tool_conf.xml
Log Message:
-----------
Upgraded dunovo on test and main, upgraded extract genomic dna on main.
1
0
27 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: db47c876ee69bd034b7e131daf0a7fd5672d2221
https://github.com/galaxyproject/galaxy/commit/db47c876ee69bd034b7e131daf0a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-14 (Wed, 14 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove prepopulation of column selector
Commit: fc7beca6d1d379ddfc1ea4769edfc8c22d74fb10
https://github.com/galaxyproject/galaxy/commit/fc7beca6d1d379ddfc1ea4769edf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-14 (Wed, 14 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Create input element combining text and select options
Commit: 2e8c9489bfd149d12b9498ea89c5633a07509d48
https://github.com/galaxyproject/galaxy/commit/2e8c9489bfd149d12b9498ea89c5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix value handling, remove redundant value check
Commit: 9fbdcd1d5ee84887c28eed727fec77d402ef95fa
https://github.com/galaxyproject/galaxy/commit/9fbdcd1d5ee84887c28eed727fec…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Relax validation conditions
Commit: ff874dc4e4f4d21bb133b2730058393c7ae7a66a
https://github.com/galaxyproject/galaxy/commit/ff874dc4e4f4d21bb133b2730058…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Properly switch between states, transfer current value
Commit: 9fff4f1615aa7ce02561d681ae20397b22b17f02
https://github.com/galaxyproject/galaxy/commit/9fff4f1615aa7ce02561d681ae20…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove redundant initial value checks, value can only be empty
Commit: 1db1c0c77122edd183ab6f0bf5da24c94c83b476
https://github.com/galaxyproject/galaxy/commit/1db1c0c77122edd183ab6f0bf5da…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Revise condition, check explicitly for none
Commit: 608f3dc9d3ed59a21fba221f590240ecfdc1294a
https://github.com/galaxyproject/galaxy/commit/608f3dc9d3ed59a21fba221f5902…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add check for column index values
Commit: f4f275f82aa9b1e19aafe0525b4006876905ef96
https://github.com/galaxyproject/galaxy/commit/f4f275f82aa9b1e19aafe0525b40…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add dataset state check to column input
Commit: a144eb1fb40eee0920e8153b3e51304c10130003
https://github.com/galaxyproject/galaxy/commit/a144eb1fb40eee0920e8153b3e51…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix integer test
Commit: 29337d2b7b1d51c44ff621049483037fd9d48d1a
https://github.com/galaxyproject/galaxy/commit/29337d2b7b1d51c44ff621049483…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Simplify legal value length check
Commit: 05ce42d229db08c6af7425f1afe1eea625dfd1da
https://github.com/galaxyproject/galaxy/commit/05ce42d229db08c6af7425f1afe1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Provide value for column index if not an integer
Commit: 9febc519944dcfb5c8907b8a302fd6aff6f0f79f
https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-15 (Thu, 15 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Identify implicit conversions, check reference context for datasets
Commit: 1baafd07ffbaa42bd5071a659ccb82203591afa0
https://github.com/galaxyproject/galaxy/commit/1baafd07ffbaa42bd5071a659ccb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-16 (Fri, 16 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Move implicit dataset tagging to dataset state check
Check attribute
Commit: dae6cc7f4cb403cdee44c532f314f639d8e9f96b
https://github.com/galaxyproject/galaxy/commit/dae6cc7f4cb403cdee44c532f314…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-16 (Fri, 16 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix indent
Commit: f305c0b0ab9182af0578078c622d024a57b9b05d
https://github.com/galaxyproject/galaxy/commit/f305c0b0ab9182af0578078c622d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-16 (Fri, 16 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Reinsert legal value check handler
Commit: c7e794745b1b7699a7ac34caaa684f298f562dbc
https://github.com/galaxyproject/galaxy/commit/c7e794745b1b7699a7ac34caaa68…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-19 (Mon, 19 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Validate value before matching dataset
Commit: 81a418fe98ee2f26b35bae81060398431b9a096e
https://github.com/galaxyproject/galaxy/commit/81a418fe98ee2f26b35bae810603…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Remove explicit integer validation
Commit: 187c540cd4aac7e1059fdaa6aaf56c87913f1d09
https://github.com/galaxyproject/galaxy/commit/187c540cd4aac7e1059fdaa6aaf5…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Fix test case
Commit: 04fee6070bfa94a3788c89dc0cc1414469db20e6
https://github.com/galaxyproject/galaxy/commit/04fee6070bfa94a3788c89dc0cc1…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M Makefile
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.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/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/visualization/visualization-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/package.json
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
A config/plugins/visualizations/scatterplot/.babelrc
M config/plugins/visualizations/scatterplot/package.json
A config/plugins/visualizations/scatterplot/src/jqglobals.js
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/scatterplot.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_shed.yml.sample
A config/workflow_resource_mapper_conf.yml.sample
A config/workflow_resource_params_conf.xml.sample
M doc/source/admin/cluster.md
M doc/source/admin/nginx.md
M doc/source/admin/scaling.md
M doc/source/releases/18.01_announce.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data_fetch.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/_fetch_util.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/modules.py
A lib/galaxy/workflow/resources/__init__.py
A lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run_request.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
A scripts/apply_tags.py
M scripts/bootstrap_history.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M test/api/test_libraries.py
M test/api/test_tools_upload.py
M test/api/test_workflows.py
M test/base/populators.py
M test/functional/tools/sample_datatypes_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
M test/integration/test_upload_configuration_options.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_to_collections.py
M test/selenium_tests/test_tool_form.py
M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml
M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/dynamic_tool_destination/ymltests.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into select_to_text
Commit: ade62bc3b15b25e76d7114c5ee9051cd5f575700
https://github.com/galaxyproject/galaxy/commit/ade62bc3b15b25e76d7114c5ee90…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Revise select display matching
Commit: 8290da24eaf0994c018b055ba9bbc73876540f7c
https://github.com/galaxyproject/galaxy/commit/8290da24eaf0994c018b055ba9bb…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Fix indentation
Commit: 241ade62cd740bf62d2348859493ed7326799597
https://github.com/galaxyproject/galaxy/commit/241ade62cd740bf62d2348859493…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-22 (Thu, 22 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Align validation order for consistency
Commit: 2b3557ffce38a97080c9921846e06131aa43e2e9
https://github.com/galaxyproject/galaxy/commit/2b3557ffce38a97080c9921846e0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Fix test case verifying we check column values before tool execution.
Commit: 91e97b60968d6813bd7a28d0d60e778b288ac385
https://github.com/galaxyproject/galaxy/commit/91e97b60968d6813bd7a28d0d60e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Refactor code for clarity
Commit: 840e436ea1f181ebe0c8478145e2cd0e97dc1778
https://github.com/galaxyproject/galaxy/commit/840e436ea1f181ebe0c8478145e2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Add strict workflow building mode check to drill downs
Commit: bf5d472e28505438c5f345ad29989b80fe3aae80
https://github.com/galaxyproject/galaxy/commit/bf5d472e28505438c5f345ad2998…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M lib/galaxy/tools/parameters/basic.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #5702 from guerler/select_to_text
Relax validation condition for dynamic parameters
Compare: https://github.com/galaxyproject/galaxy/compare/61adffbd614c...bf5d472e2850
1
0
27 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 52741200b24933d3c4af1f5a7fa5124d29d5daf6
https://github.com/galaxyproject/galaxy/commit/52741200b24933d3c4af1f5a7fa5…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
A lib/galaxy/dependencies/pinned-requirements.txt
R lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/default/Pipfile
A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
R lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Use pipenv also for the default dependencies
Commit: fb92257bc755ae12a5dad810c152967bfc68d8a1
https://github.com/galaxyproject/galaxy/commit/fb92257bc755ae12a5dad810c152…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Exclude 2 problematic h5py versions
A warning was appearing in the stderr of upload jobs due to
https://github.com/h5py/h5py/issues/995 .
Commit: f8aa29e2805b932a03a577fd329f881a3d047c98
https://github.com/galaxyproject/galaxy/commit/f8aa29e2805b932a03a577fd329f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Temporarily pin WebOb to latest compatible release
Commit: e625b649dc0e823d0c92f8c997254215bcf9dcab
https://github.com/galaxyproject/galaxy/commit/e625b649dc0e823d0c92f8c99725…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
Log Message:
-----------
Temporarily pin Mercurial to latest compatible release
Commit: 61adffbd614cbbe409f207415073604f8e13a0ba
https://github.com/galaxyproject/galaxy/commit/61adffbd614cbbe409f207415073…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
A lib/galaxy/dependencies/pinned-requirements.txt
R lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/default/Pipfile
A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
R lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Merge pull request #5786 from nsoranzo/default_pipfile
Use pipenv also for the default dependencies
Compare: https://github.com/galaxyproject/galaxy/compare/5a86b8d706b7...61adffbd614c
1
0
[galaxyproject/usegalaxy-playbook] d30a0a: Installed SnpEff version 4.3.1t on test and main.
by GitHub 27 Mar '18
by GitHub 27 Mar '18
27 Mar '18
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: d30a0a9f96d63ec2d9c83cd05b67fdcc56177bfa
https://github.com/galaxyproject/usegalaxy-playbook/commit/d30a0a9f96d63ec2…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M env/main/files/galaxy/var/integrated_tool_panel.xml
M env/main/files/galaxy/var/shed_tool_conf.xml
M env/main/files/galaxy/var/shed_tool_data_table_conf.xml
M env/test/files/galaxy/var/integrated_tool_panel.xml
M env/test/files/galaxy/var/shed_tool_conf.xml
M env/test/files/galaxy/var/shed_tool_data_table_conf.xml
Log Message:
-----------
Installed SnpEff version 4.3.1t on test and main.
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f6342616eb0b6c740b734664cc50b896ad39f4b8
https://github.com/galaxyproject/galaxy/commit/f6342616eb0b6c740b734664cc50…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-25 (Sun, 25 Mar 2018)
Changed paths:
M test/docker/base/Dockerfile
Log Message:
-----------
Fixes for testing Dockerfile recipe.
The current Dockerfile build is broken because Selenium is not compatible with the latest chromedriver it seems (and the version in galaxy/testing-base:18.01.4 isn't compatible with the latest stable Chrome - version 65). I can't get older versions of Chrome to install with the current apt source but this does at least pin the version of chromedriver.
Longer term it would be good to have the version of chrome we target to be pinned also, I hate that this Dockerfile isn't reproducible.
Commit: 5a86b8d706b7d3b8244b2359e2f7740367df1e89
https://github.com/galaxyproject/galaxy/commit/5a86b8d706b7d3b8244b2359e2f7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M test/docker/base/Dockerfile
Log Message:
-----------
Merge pull request #5693 from jmchilton/docker_test_update
Fixes for testing Dockerfile recipe.
Compare: https://github.com/galaxyproject/galaxy/compare/f14c6ffe49b3...5a86b8d706b7
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[galaxyproject/galaxy] 412ff1: Add config rebuild left out of migration of option...
by GitHub 27 Mar '18
by GitHub 27 Mar '18
27 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 412ff1e16ae50af06751d3aae936973ef954fc61
https://github.com/galaxyproject/galaxy/commit/412ff1e16ae50af06751d3aae936…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M doc/source/admin/galaxy_options.rst
Log Message:
-----------
Add config rebuild left out of migration of options from 18.01 (I think)
Commit: f14c6ffe49b397b884f678812f311fc0bd451e53
https://github.com/galaxyproject/galaxy/commit/f14c6ffe49b397b884f678812f31…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M doc/source/admin/galaxy_options.rst
Log Message:
-----------
Merge pull request #5788 from dannon/configrebuild
Config-rebuild w/ options doc
Compare: https://github.com/galaxyproject/galaxy/compare/39d5ec89f885...f14c6ffe49b3
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27 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb
https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths:
M config/galaxy.yml.sample
M config/reports.yml.sample
M config/tool_shed.yml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/reports_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
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Fix type of some options in config_schema.yml
Also:
- drop unused `nginx_x_archive_files_base` option, last use removed in
commit fe5983aafca1fae0b60ed16838799b58f4aca11c
- rebuild config samples and docs.
Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8
https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths:
M lib/galaxy/webapps/config_manage.py
Log Message:
-----------
Don't quote ints in .ini to .yml config conversion
Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475
https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths:
M lib/galaxy/tools/actions/model_operations.py
M test/api/test_tools.py
Log Message:
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Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03
Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB.
Includes test case that fails against 18.01.
Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412
https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M lib/galaxy/tools/actions/model_operations.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #5784 from jmchilton/1801_fix_unzip
[18.01] Fix model operation tools that produce standalone datasets.
Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce
https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M config/galaxy.yml.sample
M config/reports.yml.sample
M config/tool_shed.yml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/reports_options.rst
M lib/galaxy/config.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message:
-----------
Merge pull request #5745 from nsoranzo/release_18.01_fix_config
[18.01] Configuration fixes
Commit: 39d5ec89f885ffce8e3c9621439c76d9d0745aa6
https://github.com/galaxyproject/galaxy/commit/39d5ec89f885ffce8e3c9621439c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths:
M config/galaxy.yml.sample
M doc/source/admin/galaxy_options.rst
M lib/galaxy/config.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M test/api/test_tools.py
Log Message:
-----------
Merge branch 'release_18.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/45dd9889654c...39d5ec89f885
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