galaxy-commits
Threads by month
- ----- 2024 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2023 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2022 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2021 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2020 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2019 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2018 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2017 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2016 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2015 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2014 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2013 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2012 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2011 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2010 -----
- December
- November
- October
- September
- August
- July
- June
- May
October 2016
- 1 participants
- 98 discussions
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: c6b3998b3b084aa60958153f4e08a823fa1555b1
https://github.com/galaxyproject/usegalaxy-playbook/commit/c6b3998b3b084aa6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-10-20 (Thu, 20 Oct 2016)
Changed paths:
M production/galaxy_version.yml
Log Message:
-----------
Update Main
1
0
[galaxyproject/galaxy] 3a99bb: Add deprecated, legacy attribute default_value to ...
by GitHub 19 Oct '16
by GitHub 19 Oct '16
19 Oct '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3a99bbae0716c98aa8e8d290a666909ac88c0817
https://github.com/galaxyproject/galaxy/commit/3a99bbae0716c98aa8e8d290a666…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Add deprecated, legacy attribute default_value to XSD.
Cleanup use of ``gxdocs:deprecated``.
Commit: 05f792edcd4bf779d0e9c91f5f4c92396979f17b
https://github.com/galaxyproject/galaxy/commit/05f792edcd4bf779d0e9c91f5f4c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Specify actual parameter to use in lieu of default_value in XSD.
As suggested by @nsoranzo.
Commit: cfeb0135ac5fc3334d5a3afcfdfd1e586ce5d32f
https://github.com/galaxyproject/galaxy/commit/cfeb0135ac5fc3334d5a3afcfdfd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-19 (Wed, 19 Oct 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #3072 from jmchilton/default_value_legacy_xsd
Add deprecated, legacy attribute default_value to XSD.
Compare: https://github.com/galaxyproject/galaxy/compare/2a7e4f79c0c0...cfeb0135ac5f
1
0
[galaxyproject/galaxy] bdc882: Dataset metadata should not be cached when buildin...
by GitHub 18 Oct '16
by GitHub 18 Oct '16
18 Oct '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: bdc8829dd2363c759b362a275757448173afcd22
https://github.com/galaxyproject/galaxy/commit/bdc8829dd2363c759b362a275757…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/static/client/app.js
Log Message:
-----------
Dataset metadata should not be cached when building chart visualizations
Commit: 2a7e4f79c0c04158fe37dbd6c1b95cc251537173
https://github.com/galaxyproject/galaxy/commit/2a7e4f79c0c04158fe37dbd6c1b9…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/static/client/app.js
Log Message:
-----------
Merge pull request #3062 from guerler/fix_dataset_caching
Dataset metadata should not be cached when building chart visualizations
Compare: https://github.com/galaxyproject/galaxy/compare/569723a4e548...2a7e4f79c0c0
1
0
18 Oct '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3e737c99ea21dcb7ea3a326d36aee9c715c8d70b
https://github.com/galaxyproject/galaxy/commit/3e737c99ea21dcb7ea3a326d36ae…
Author: Remi Marenco <remi.marenco(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M .gitignore
M Makefile
M doc/source/conf.py
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/model/migrate/check.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
Log Message:
-----------
Add Galaxy Architecture slides in .md
+ the plumbing for slides creation
Init of #2244, second part: Python converter md to html + wip on GCC 2015 talk conversion
Add the 2. Galaxy app architecture. Need images
Add the 3. Galaxy components and object model
Add more content in md
Fix linting error by adding newline at the end of build_slideshow.py
Moved the galaxyArchitecture.md into a folder dedicated to it
Add 7th and 17th image + add style.css to have a better management of layout + added first slide as the first in GCC2015 slide
Set properly the CSS used in the whole presentation + add special to p and first slide
Add special orange for regular text and green emphasis (emphasis_2_galaxy)
Changed the font to PT Sans
Add 3. with images + few modifications
Removed the images integrated using background-image by now Markdown imaging (still need work, image's size seems not good by default
Add Makefile target to build architecture slides...
2016 Updates to 2015 architecture talk.
More intro slides for Galaxy architecture.
Update author line.
Progress on architecture slides...
- Improved styling (use Oxygen - closer to Galaxy font)
- Add ability to generate SVG diagrams to slide infrastructure
- Add newer client-server sequence diagram based on that.
Improved logging when there are problems with SQL migrations.
More misc work on architecture talk.
More images, slides, slide formatting, and initial work on an IPython notebook.
Improved styling for architecture slides...
Updates to architecture talk...
- Infrastructure for building class diagrams with plantuml
- Bring in move SVGs from last year's google docs.
- Fill out section on client architecture.
More work on slides for architecture talk.
Add startup_output.
Replace mermaid diagrams with plantuml diagrams.
Fill out these diagrams more and style them for a black background in Galaxy oranges.
Commit: 564aeeccd7379a5717de2180f5eb3208e479ea98
https://github.com/galaxyproject/galaxy/commit/564aeeccd7379a5717de2180f5eb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M Makefile
Log Message:
-----------
remove the duplicated variable
Commit: 569723a4e5487c4eab25dfe619cda5b044b6115b
https://github.com/galaxyproject/galaxy/commit/569723a4e5487c4eab25dfe619cd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-18 (Tue, 18 Oct 2016)
Changed paths:
M .gitignore
M Makefile
M doc/source/conf.py
A doc/source/slideshow/architecture/galaxy_architecture.md
A doc/source/slideshow/architecture/images/backbone-model-view.svg
A doc/source/slideshow/architecture/images/cluster_support.svg
A doc/source/slideshow/architecture/images/data_managers.svg
A doc/source/slideshow/architecture/images/docker-chart.png
A doc/source/slideshow/architecture/images/family/team.png
A doc/source/slideshow/architecture/images/galaxy_schema.png
A doc/source/slideshow/architecture/images/hda.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
A doc/source/slideshow/architecture/images/hda_dataset.plantuml.txt
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
A doc/source/slideshow/architecture/images/hda_hdca.plantuml.txt
A doc/source/slideshow/architecture/images/jsload.png
A doc/source/slideshow/architecture/images/libraries.svg
A doc/source/slideshow/architecture/images/library_permissions.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.svg
A doc/source/slideshow/architecture/images/objectstore.plantuml.txt
A doc/source/slideshow/architecture/images/objectstore_diagram.svg
A doc/source/slideshow/architecture/images/plantuml_options.txt
A doc/source/slideshow/architecture/images/sequence.json
A doc/source/slideshow/architecture/images/server_client.plantuml.svg
A doc/source/slideshow/architecture/images/server_client.plantuml.txt
A doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
A doc/source/slideshow/architecture/images/server_client_old.plantuml.txt
A doc/source/slideshow/architecture/images/sqla_arch_small.png
A doc/source/slideshow/architecture/images/usegalaxy_webservers.svg
A doc/source/slideshow/architecture/images/usegalaxyorg.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.svg
A doc/source/slideshow/architecture/images/webapp.plantuml.txt
A doc/source/slideshow/architecture/images/what-is-webpack.svg
A doc/source/slideshow/architecture/images/workflow_definition.svg
A doc/source/slideshow/architecture/images/workflow_run.svg
A doc/source/slideshow/architecture/images/wsgi_app.svg
A doc/source/slideshow/architecture/images/wsgi_request.svg
A doc/source/slideshow/architecture/remark-latest.min.js
A doc/source/slideshow/architecture/style.css
M lib/galaxy/model/migrate/check.py
A scripts/slideshow/__init__.py
A scripts/slideshow/build_slideshow.py
A scripts/slideshow/example.md
A scripts/slideshow/slideshow_template.html
A scripts/slideshow/style.sample.css
Log Message:
-----------
Merge pull request #3060 from martenson/remimarenco-gcc2015_talk
Add Galaxy Architecture slides in .md
Compare: https://github.com/galaxyproject/galaxy/compare/1dc2d6a4ead3...569723a4e548
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8e0eaf2427a99f093a35d686532214534c1bb043
https://github.com/galaxyproject/galaxy/commit/8e0eaf2427a99f093a35d6865322…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/config/charts.xml
A config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
A config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js
M config/plugins/visualizations/charts/static/charts/overview.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add biojs multiple sequence viewer
Commit: 97519231e536ab689d5285ce328c46e19fa2566b
https://github.com/galaxyproject/galaxy/commit/97519231e536ab689d5285ce328c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
Log Message:
-----------
Fix style
Commit: 6a450b9a06a81a58875297af7832f1d5a2cab8a5
https://github.com/galaxyproject/galaxy/commit/6a450b9a06a81a58875297af7832…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js
Log Message:
-----------
Add basic options to configure msa viewer
Commit: 72ea2b030242cf448829f82d02e77a10ef7ce75d
https://github.com/galaxyproject/galaxy/commit/72ea2b030242cf448829f82d02e7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
M config/plugins/visualizations/charts/static/components/jobs.js
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Avoid parsing app to chart wrappers
Commit: e02eb60296eac4339aa2265313a38d4dc36aa415
https://github.com/galaxyproject/galaxy/commit/e02eb60296eac4339aa2265313a3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/storage.js
Log Message:
-----------
Decouple storage, parse parameters explicitly
Commit: 37c1e316a74348ad1023bd071f19e4396758540a
https://github.com/galaxyproject/galaxy/commit/37c1e316a74348ad1023bd071f19…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/storage.js
Log Message:
-----------
Move chart listener into storage
Commit: 48ff0790bf9b2115d891ca4c1a375f7f266b3399
https://github.com/galaxyproject/galaxy/commit/48ff0790bf9b2115d891ca4c1a37…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/storage.js
Log Message:
-----------
Fix save failed message
Commit: 3048b56006cc1ee0877e24767e2535ccbe5164b7
https://github.com/galaxyproject/galaxy/commit/3048b56006cc1ee0877e24767e25…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Remove unused container list
Commit: a63b07795c23a7412592d8aa7e395ff6394625ae
https://github.com/galaxyproject/galaxy/commit/a63b07795c23a7412592d8aa7e39…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Fix scrolling behavior
Commit: f2c1e23409f407b773913629714c697a04fb0740
https://github.com/galaxyproject/galaxy/commit/f2c1e23409f407b773913629714c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/overview.js
M config/plugins/visualizations/charts/static/views/viewer.js
Log Message:
-----------
Add description for biojs
Commit: 7107705b9c821c20a07ae3275c50eac517b44a37
https://github.com/galaxyproject/galaxy/commit/7107705b9c821c20a07ae3275c50…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Remove unused menu div
Commit: 5f642113156435b34d3ff6de01144069d2e370c1
https://github.com/galaxyproject/galaxy/commit/5f642113156435b34d3ff6de0114…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Use shorter dom query command
Commit: ebd0dab936b4fbb82dbb21218851ca7579197bf7
https://github.com/galaxyproject/galaxy/commit/ebd0dab936b4fbb82dbb21218851…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Change draw label to indicate that the chart will be saved too
Commit: 30bd72310e4d51f49e9fe020b119c02642ffe854
https://github.com/galaxyproject/galaxy/commit/30bd72310e4d51f49e9fe020b119…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix tooltip
Commit: 9481939154269253e59a2d9ffafe506947287dc1
https://github.com/galaxyproject/galaxy/commit/9481939154269253e59a2d9ffafe…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
M config/plugins/visualizations/charts/static/views/settings.js
Log Message:
-----------
Remove separated tabular input element
Commit: 70e68c204b3f250e76032761d796f62552f63d70
https://github.com/galaxyproject/galaxy/commit/70e68c204b3f250e76032761d796…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/settings.js
Log Message:
-----------
Fix spacing
Commit: 77dddc3fa42e28eef9ad14c30d8047b2b2865c09
https://github.com/galaxyproject/galaxy/commit/77dddc3fa42e28eef9ad14c30d80…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/settings.js
Log Message:
-----------
Generalize internal use panels parameter option
Commit: d6f174e487b77862c005b65843af79c53bd560c7
https://github.com/galaxyproject/galaxy/commit/d6f174e487b77862c005b65843af…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/views/viewer.js
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Filter exportable datatypes by chart type
Commit: 6d28721158e9e385c5d734de280eb4c9d3386672
https://github.com/galaxyproject/galaxy/commit/6d28721158e9e385c5d734de280e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Repack
Commit: 6c0df63e255c198380ca1e168ebed87a8467924f
https://github.com/galaxyproject/galaxy/commit/6c0df63e255c198380ca1e168ebe…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/viewer.js
Log Message:
-----------
Fix tooltip
Commit: 004fbd6e551a8fbd3bc9f9317ca34b4f55e10ea4
https://github.com/galaxyproject/galaxy/commit/004fbd6e551a8fbd3bc9f9317ca3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/others/example/config.js
Log Message:
-----------
Fix developer examples config
Commit: 9e2e0dc7394814066c98b65e990e5a3750b9756e
https://github.com/galaxyproject/galaxy/commit/9e2e0dc7394814066c98b65e990e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
Log Message:
-----------
Fix developer example
Commit: e8eb48a9c42de08edd6e9a4ea529bcac0d698df9
https://github.com/galaxyproject/galaxy/commit/e8eb48a9c42de08edd6e9a4ea529…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Remove unused app variable
Commit: f98ade125f0fbe5d90ca0f005a84f8f7d91fb3d5
https://github.com/galaxyproject/galaxy/commit/f98ade125f0fbe5d90ca0f005a84…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
Log Message:
-----------
Add basic description for msa viewer
Commit: c4e9ecfe4c9dec4f9c58597fc755a4c4ab944a83
https://github.com/galaxyproject/galaxy/commit/c4e9ecfe4c9dec4f9c58597fc755…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/others/example/config.js
M config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Allow multiple datatype matching
Commit: edfdef2853e2df3f5058d97e1578c4129fb292de
https://github.com/galaxyproject/galaxy/commit/edfdef2853e2df3f5058d97e1578…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M static/maps/mvc/ui/ui-buttons.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-buttons.js
Log Message:
-----------
Enhance ui menu button view
Commit: 72f89a4c262de328d398ebbb4c6ccfefc483b75d
https://github.com/galaxyproject/galaxy/commit/72f89a4c262de328d398ebbb4c6c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Fix requirements message
Commit: 59852d0e0f4897b09a964091d5792458de48deb0
https://github.com/galaxyproject/galaxy/commit/59852d0e0f4897b09a964091d579…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/biojs/msa/config.js
R config/plugins/visualizations/charts/static/charts/biojs/msa/logo.png
R config/plugins/visualizations/charts/static/charts/biojs/msa/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/components/jobs.js
R config/plugins/visualizations/charts/static/plugins/biojs/biojs.msa.js
R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js
R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js
R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
M config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Use remote repo for chart plugins
Commit: af45adb7e6e57d4180b49581c5f48274df54117f
https://github.com/galaxyproject/galaxy/commit/af45adb7e6e57d4180b49581c5f4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add error message if charts fails to retrieve plugin resources from its repository
Commit: 3e7302fc3c6d8f0713d8698f6536662fc46f42b0
https://github.com/galaxyproject/galaxy/commit/3e7302fc3c6d8f0713d8698f6536…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Fix remote url
Commit: 42854e31ea50eae1e26ce2112696cd86ccb247be
https://github.com/galaxyproject/galaxy/commit/42854e31ea50eae1e26ce2112696…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Bundle thumbnail view
Commit: d4d403d678a9c6d5a5dbf1df5c23b8425f1a1311
https://github.com/galaxyproject/galaxy/commit/d4d403d678a9c6d5a5dbf1df5c23…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Show list instead
Commit: 6f444e5cdbc69ba0fdca4a04c1dce7d7493420be
https://github.com/galaxyproject/galaxy/commit/6f444e5cdbc69ba0fdca4a04c1dc…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Restore regular selection view
Commit: ccd265ed0705d3166f792d7d1473f229c8b5accb
https://github.com/galaxyproject/galaxy/commit/ccd265ed0705d3166f792d7d1473…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix tab creation behavior
Commit: d65bf1e4f773c6c6d27b83e7a850b51bfd3d3faa
https://github.com/galaxyproject/galaxy/commit/d65bf1e4f773c6c6d27b83e7a850…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix sorting
Commit: bee75fb77909ddc938290c134eb689a7f5729254
https://github.com/galaxyproject/galaxy/commit/bee75fb77909ddc938290c134eb6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix order
Commit: 9601a0f607b71e8725dafff90288ee8486dbfcf1
https://github.com/galaxyproject/galaxy/commit/9601a0f607b71e8725dafff90288…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Revise thumbnail view
Commit: ec038cb0904b24c6df8cb5f7b16e671997004aa7
https://github.com/galaxyproject/galaxy/commit/ec038cb0904b24c6df8cb5f7b16e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Use original order
Commit: 5cae6f7735436800c586065be690a43c1a1683e5
https://github.com/galaxyproject/galaxy/commit/5cae6f7735436800c586065be690…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Fix spacing
Commit: 71fe20ab040df9393c8ac0c083a31006a65ab848
https://github.com/galaxyproject/galaxy/commit/71fe20ab040df9393c8ac0c083a3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M client/galaxy/scripts/utils/utils.js
M config/plugins/visualizations/charts/static/views/description.js
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/utils/utils.js
Log Message:
-----------
Identify links in visualizations plugins descriptions
Commit: e0617bb29b280f5f7f756ccbfdd6678ed3e185ef
https://github.com/galaxyproject/galaxy/commit/e0617bb29b280f5f7f756ccbfdd6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Add tooltip to thumbnail view?
Commit: f03a06488feb0e1c471c92d11cff14c6bf5c0cf1
https://github.com/galaxyproject/galaxy/commit/f03a06488feb0e1c471c92d11cff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Limit title length for thumbnails
Commit: f2b26a61cb14ff468ecc2971d6394e6cea64f889
https://github.com/galaxyproject/galaxy/commit/f2b26a61cb14ff468ecc2971d639…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Filter suitable visualization types on initialization
Commit: 84942582b57499a753cf9e8039486c3bc9efa4f3
https://github.com/galaxyproject/galaxy/commit/84942582b57499a753cf9e803948…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
Log Message:
-----------
Modify error message
Commit: 3e79da902163b131aff677a7b1bad9fa87e61d89
https://github.com/galaxyproject/galaxy/commit/3e79da902163b131aff677a7b1ba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Fix error messages
Commit: 5d780d68d1a2ec5d1928a0156637a1d522f5b743
https://github.com/galaxyproject/galaxy/commit/5d780d68d1a2ec5d1928a0156637…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/screenshot.js
Log Message:
-----------
Revise exporting functions, increase png quality, remove unused libraries
Commit: 78bd9e8f867eb5747218644e2a5a1f5417079b73
https://github.com/galaxyproject/galaxy/commit/78bd9e8f867eb5747218644e2a5a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M Makefile
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
R database/info.txt
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M scripts/bootstrap_history.py
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/index.mako
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: a97b4bae546a5621dc37b6beaaba747d51c8ed9e
https://github.com/galaxyproject/galaxy/commit/a97b4bae546a5621dc37b6beaaba…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
Log Message:
-----------
Rename types to registry to avoid confusion
Commit: 494141c260514071c5187a83a8dd1700643b5423
https://github.com/galaxyproject/galaxy/commit/494141c260514071c5187a83a8dd…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Use underscores for internal parameters to avoid conflicts
Commit: 61839637f098130ccd54bfe408ff9955dbffc883
https://github.com/galaxyproject/galaxy/commit/61839637f098130ccd54bfe408ff…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/storage.js
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Simplify storage handling
Commit: 7d20e9055e1be434c7914fc540ceb64a8e4d1051
https://github.com/galaxyproject/galaxy/commit/7d20e9055e1be434c7914fc540ce…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
Log Message:
-----------
Remove unused options variable
Commit: 30d4e338b473797816e8b8a5da93dcd5420e24fc
https://github.com/galaxyproject/galaxy/commit/30d4e338b473797816e8b8a5da93…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Revise visualization config handling
Commit: 57b41b201964b57daf9a95c06120cbe1bba14e1b
https://github.com/galaxyproject/galaxy/commit/57b41b201964b57daf9a95c06120…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
Log Message:
-----------
Fix chart saving
Commit: 22e79f7aa943edb9ca6a80d1b035931ab8c9232f
https://github.com/galaxyproject/galaxy/commit/22e79f7aa943edb9ca6a80d1b035…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Improve handling for cases with missing plugins
Commit: 76c9948742d659b2dd73452cc2d3c49f44f00cd7
https://github.com/galaxyproject/galaxy/commit/76c9948742d659b2dd73452cc2d3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Enhance notification and handling when chart type is unavailable
Commit: 81dffca58cab841dfcf0fda42b42d5c97f54f245
https://github.com/galaxyproject/galaxy/commit/81dffca58cab841dfcf0fda42b42…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Remove test case, replace change listeners
Commit: fa7930d20e10309aee666f280963b759571e3884
https://github.com/galaxyproject/galaxy/commit/fa7930d20e10309aee666f280963…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix message persistence for missing column notification
Commit: b3451ed03d5104442b4935905e330b006e492204
https://github.com/galaxyproject/galaxy/commit/b3451ed03d5104442b4935905e33…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix message persistence for missing data groups
Commit: 4669d5ee26410faec0c6e49aed512352631066e3
https://github.com/galaxyproject/galaxy/commit/4669d5ee26410faec0c6e49aed51…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Remove warning notification when leaving charts, data is saved upon drawing
Commit: 00053b6d30b21ce2eed5419a3537caa0b8cd7797
https://github.com/galaxyproject/galaxy/commit/00053b6d30b21ce2eed5419a3537…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
Log Message:
-----------
Fix spacing
Commit: ffba835195737c4705e5b2717c384be05edeae91
https://github.com/galaxyproject/galaxy/commit/ffba835195737c4705e5b2717c38…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Remove spacing
Commit: 7351d67967a0750a5e351660b457d92dcb01b516
https://github.com/galaxyproject/galaxy/commit/7351d67967a0750a5e351660b457…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/types.js
Log Message:
-----------
Remove unused listener
Commit: 05fa9b9f5adcd96456348754225c72554d4e12af
https://github.com/galaxyproject/galaxy/commit/05fa9b9f5adcd96456348754225c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Rename remote to repository to avoid confusion
Commit: 3d9df6437073484d243d64fc9606dc137dc6bfb7
https://github.com/galaxyproject/galaxy/commit/3d9df6437073484d243d64fc9606…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Rename optional config attributes name accordingly
Commit: ff301c562b87a1843d18819eb79dd580d207e9c8
https://github.com/galaxyproject/galaxy/commit/ff301c562b87a1843d18819eb79d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/app.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add debug log, fix config name, add comment for local repository
Commit: 36c1384d020bcb2d3a89da83861cccfae23e8916
https://github.com/galaxyproject/galaxy/commit/36c1384d020bcb2d3a89da83861c…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Use rawgit for proper MIME type handling
Commit: 819cb65d2e1ecc905b22e97b9972fa8901ac09c1
https://github.com/galaxyproject/galaxy/commit/819cb65d2e1ecc905b22e97b9972…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Add repository revision to url
Commit: d5440f7ac4170adf27f757fdfbc888a67e20cf27
https://github.com/galaxyproject/galaxy/commit/d5440f7ac4170adf27f757fdfbc8…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository version, allow pdb rendering type selection
Commit: 14ef3e3d448dc4190707312443b6f60e187ee962
https://github.com/galaxyproject/galaxy/commit/14ef3e3d448dc4190707312443b6…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository version
Commit: d98a72d58e1cf462eb89f4a9cd3e04a5c6fea9fb
https://github.com/galaxyproject/galaxy/commit/d98a72d58e1cf462eb89f4a9cd3e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A database/info.txt
M doc/source/admin/conda_faq.rst
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/deps/resolvers/conda.py
R lib/galaxy/tools/toolbox/requirements.py
A lib/galaxy/util/filelock.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M static/maps/layout/menu.js.map
M static/scripts/bundled/libs.bundled.js.map
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 14c0365b22d238e8c48b20dc64654cc412386059
https://github.com/galaxyproject/galaxy/commit/14c0365b22d238e8c48b20dc6465…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-08 (Thu, 08 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository revision
Commit: 5e8a2ced3a819a238227bbde0627d90cfd3cf728
https://github.com/galaxyproject/galaxy/commit/5e8a2ced3a819a238227bbde0627…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/viewer.js
Log Message:
-----------
Distinguish draw and save to avoid accumulation of saved visualizations
Commit: cf9db96a1d7076474873c5b1f6e7ed2e32a3d79e
https://github.com/galaxyproject/galaxy/commit/cf9db96a1d7076474873c5b1f6e7…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Change label from draw to visualize
Commit: a88942b0875f659e799d65bd00cea1d771c82570
https://github.com/galaxyproject/galaxy/commit/a88942b0875f659e799d65bd00ce…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/components/model.js
M config/plugins/visualizations/charts/static/components/screenshot.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/viewer.js
Log Message:
-----------
Unify labels and tooltips
Commit: 052b6e367bdeeffa5811853612a3bb1759c27039
https://github.com/galaxyproject/galaxy/commit/052b6e367bdeeffa5811853612a3…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-09 (Fri, 09 Sep 2016)
Changed paths:
M config/plugins/visualizations/charts/static/views/editor.js
Log Message:
-----------
Fix tooltip
Commit: 8b13f63f423800bf17e51a99231fa35099b58519
https://github.com/galaxyproject/galaxy/commit/8b13f63f423800bf17e51a99231f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-14 (Wed, 14 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .gitignore
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dockerfiles.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M setup.cfg
M templates/show_params.mako
M templates/webapps/galaxy/workflow/run.mako
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M tools/data_source/upload.xml
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 46d05ba08017cf10467eb0334272e48733c9f684
https://github.com/galaxyproject/galaxy/commit/46d05ba08017cf10467eb0334272…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
A doc/parse_gx_xsd.py
A doc/schema_template.md
M doc/source/project/issues.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/toolbox/base.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/base/interactor.py
A test/functional/tools/metadata_column_names.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/qunit/tests/form_tests.js
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/unittest_utils/galaxy_mock.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 494d50f52c33a7465e0d466a3e43fba9fd5a1dbd
https://github.com/galaxyproject/galaxy/commit/494d50f52c33a7465e0d466a3e43…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-09-29 (Thu, 29 Sep 2016)
Changed paths:
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/mvc/tool/tool-form-base.js
Log Message:
-----------
Repack client
Commit: fdc81bd84a76082249474782367b7b7a59706af3
https://github.com/galaxyproject/galaxy/commit/fdc81bd84a76082249474782367b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Upgrade repository revision
Commit: 2316075f0caf7771bafabbfa00bfe2c5ecdfacec
https://github.com/galaxyproject/galaxy/commit/2316075f0caf7771bafabbfa00bf…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M config/job_conf.xml.sample_advanced
M doc/source/admin/conda_faq.rst
M doc/source/api/guidelines.rst
M lib/galaxy/datatypes/data.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M scripts/bootstrap_history.py
M setup.cfg
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-modal.js
A test/api/test_workflow_batch.ga
M test/api/test_workflows.py
M test/base/driver_util.py
A test/functional/tools/color_param.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: b7a25fc653fa30a78d97b2aa23e9a5ad43814694
https://github.com/galaxyproject/galaxy/commit/b7a25fc653fa30a78d97b2aa23e9…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-08 (Sat, 08 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Update repository revision to new drawrnajs logo
Commit: bf5cc30b843838f30a4b40faa9834cbc28a01991
https://github.com/galaxyproject/galaxy/commit/bf5cc30b843838f30a4b40faa983…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
R config/plugins/visualizations/charts/sample.txt
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/viewport.js
Log Message:
-----------
Remove tabular file from repo, fix comments
Commit: 1805ac8b5948ded11e154c887a2da99481ac70c6
https://github.com/galaxyproject/galaxy/commit/1805ac8b5948ded11e154c887a2d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
A config/plugins/visualizations/charts/static/client/app.css
A config/plugins/visualizations/charts/static/client/app.js
A config/plugins/visualizations/charts/static/client/components/model.js
A config/plugins/visualizations/charts/static/client/components/screenshot.js
A config/plugins/visualizations/charts/static/client/views/description.js
A config/plugins/visualizations/charts/static/client/views/editor.js
A config/plugins/visualizations/charts/static/client/views/groups.js
A config/plugins/visualizations/charts/static/client/views/settings.js
A config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/client/views/viewer.js
A config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
A config/plugins/visualizations/charts/static/repository/build/others_example.js
A config/plugins/visualizations/charts/static/repository/build/others_example.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.js
A config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
Log Message:
-----------
Add chart plugins back to plugins directory of visualization framework
Commit: f467384fdd97dba43ee0f9b7c3592498de738ee8
https://github.com/galaxyproject/galaxy/commit/f467384fdd97dba43ee0f9b7c359…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/templates/charts.mako
Log Message:
-----------
Use fixed repository path
Commit: fe73009db5248a04844db86584064b48a86f2cb2
https://github.com/galaxyproject/galaxy/commit/fe73009db5248a04844db8658406…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M config/plugins/visualizations/charts/static/client/components/model.js
Log Message:
-----------
Fix default options for storing request
Commit: f053f9bb3d2820c09aab1a0bc3b29e27eed56d09
https://github.com/galaxyproject/galaxy/commit/f053f9bb3d2820c09aab1a0bc3b2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .travis.yml
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M doc/parse_gx_xsd.py
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/checkers.py
A lib/galaxy/util/image_util.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M static/maps/mvc/tool/tools.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tools.js
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_runner_local.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
M tools/data_source/upload.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge branch 'dev' into remote_chart_plugins
Commit: 1dc2d6a4ead34b9d8bdaecf85f146ca17b5e803c
https://github.com/galaxyproject/galaxy/commit/1dc2d6a4ead34b9d8bdaecf85f14…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/utils/utils.js
R config/plugins/visualizations/charts/Gruntfile.js
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/sample.txt
R config/plugins/visualizations/charts/static/app.css
R config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/example/config.js
R config/plugins/visualizations/charts/static/charts/others/example/logo.png
R config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/charts/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/types.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
R config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/client/app.css
A config/plugins/visualizations/charts/static/client/app.js
A config/plugins/visualizations/charts/static/client/components/model.js
A config/plugins/visualizations/charts/static/client/components/screenshot.js
A config/plugins/visualizations/charts/static/client/views/description.js
A config/plugins/visualizations/charts/static/client/views/editor.js
A config/plugins/visualizations/charts/static/client/views/groups.js
A config/plugins/visualizations/charts/static/client/views/settings.js
A config/plugins/visualizations/charts/static/client/views/types.js
A config/plugins/visualizations/charts/static/client/views/viewer.js
A config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/components/jobs.js
R config/plugins/visualizations/charts/static/components/model.js
R config/plugins/visualizations/charts/static/components/screenshot.js
R config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/plugins/canvg/canvg.js
R config/plugins/visualizations/charts/static/plugins/canvg/rgbcolor.js
R config/plugins/visualizations/charts/static/plugins/crossfilter/crossfilter.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.barRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.blockRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.boxplotRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasOverlay.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.canvasTextRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.categoryAxisRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.cursor.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.enhancedLegendRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.highlighter.min.js
R config/plugins/visualizations/charts/static/plugins/jqplot/plugins/jqplot.ohlcRenderer.min.js
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
A config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
A config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
A config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
A config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
A config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
A config/plugins/visualizations/charts/static/repository/build/others_example.js
A config/plugins/visualizations/charts/static/repository/build/others_example.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
A config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
A config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.js
A config/plugins/visualizations/charts/static/repository/build/registry.js.map
A config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
A config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
A config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
A config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
A config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
A config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
A config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/jobs.js
A config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/static/views/description.js
R config/plugins/visualizations/charts/static/views/editor.js
R config/plugins/visualizations/charts/static/views/groups.js
R config/plugins/visualizations/charts/static/views/settings.js
R config/plugins/visualizations/charts/static/views/types.js
R config/plugins/visualizations/charts/static/views/viewer.js
R config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A config/plugins/visualizations/charts/webpack.config.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/utils/utils.js
Log Message:
-----------
Merge pull request #2875 from guerler/remote_chart_plugins
Link charts to external repo, adjust interface
Compare: https://github.com/galaxyproject/galaxy/compare/7eb413f4e8ee...1dc2d6a4ead3
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5549a9ee2bd01940254c49e58ab143d4aa95049a
https://github.com/galaxyproject/galaxy/commit/5549a9ee2bd01940254c49e58ab1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Fix link in galaxy.xsd.
Commit: e8f35310ba581e8f88d719053979c4c3603c930a
https://github.com/galaxyproject/galaxy/commit/e8f35310ba581e8f88d719053979…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M doc/schema_template.md
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Revise and improve ``version_command`` tag.
- Include deprecated ``interpreter`` tag in XSD. (Closes galaxyproject/planemo#574)
- Allow the use of ``$__tool_directory__`` in interpreter command (so we can actually call ``interpreter`` deprecated).
- Include sample tools of both of these styles.
- General improvements to the version command documentation.
Commit: 7eb413f4e8ee97d68a6fa466d9c5189b324dde52
https://github.com/galaxyproject/galaxy/commit/7eb413f4e8ee97d68a6fa466d9c5…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M doc/schema_template.md
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/version_command.py
A test/functional/tools/version_command_interpreter.xml
A test/functional/tools/version_command_plain.xml
A test/functional/tools/version_command_tool_dir.xml
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Merge pull request #2961 from jmchilton/xsd_fixes_1
Improve ``version_command`` tag.
Compare: https://github.com/galaxyproject/galaxy/compare/22839eeee0b0...7eb413f4e8ee
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 868658c7e72e3d0f37e36c51316a72a56a270376
https://github.com/galaxyproject/galaxy/commit/868658c7e72e3d0f37e36c51316a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-14 (Fri, 14 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Always display text, with test cases
Commit: 22839eeee0b0909bc2726e60ffb26a213ddfc553
https://github.com/galaxyproject/galaxy/commit/22839eeee0b0909bc2726e60ffb2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #3052 from guerler/always_display_text
Always display text
Compare: https://github.com/galaxyproject/galaxy/compare/7207c1509038...22839eeee0b0
1
0
[galaxyproject/galaxy] d93ced: Increase min number of columns for pileup sniffing...
by GitHub 17 Oct '16
by GitHub 17 Oct '16
17 Oct '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d93cedef8a3e727bc0a089ad6eda4c5734cd55c7
https://github.com/galaxyproject/galaxy/commit/d93cedef8a3e727bc0a089ad6eda…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Increase min number of columns for pileup sniffing to 5
Fix #3001.
Commit: 3be66005dc4cbd2a7d45e2a482f297dcaf493c02
https://github.com/galaxyproject/galaxy/commit/3be66005dc4cbd2a7d45e2a482f2…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-11 (Tue, 11 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Check that chromosome number is >=0
Commit: 7207c15090385a397493da0503b06dbea1004d68
https://github.com/galaxyproject/galaxy/commit/7207c15090385a397493da0503b0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/tabular.py
Log Message:
-----------
Merge pull request #3033 from nsoranzo/fix_for_3001
Increase min number of columns for pileup sniffing to 5
Compare: https://github.com/galaxyproject/galaxy/compare/4bf1994fc3fd...7207c1509038
1
0
[galaxyproject/galaxy] 762337: Fix import orders for updates to flake8_import_ord...
by GitHub 17 Oct '16
by GitHub 17 Oct '16
17 Oct '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 762337e110d7a8d4058d7fcc7fd41147b0d89020
https://github.com/galaxyproject/galaxy/commit/762337e110d7a8d4058d7fcc7fd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Fix import orders for updates to flake8_import_order.
Commit: 4bf1994fc3fd09b874c9ea29a8871269d44ad193
https://github.com/galaxyproject/galaxy/commit/4bf1994fc3fd09b874c9ea29a887…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/web/framework/middleware/static.py
M lib/galaxy/webapps/galaxy/api/tours.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
M test/api/test_histories.py
M test/api/test_libraries.py
M test/unit/tools/test_tool_dependency_description.py
Log Message:
-----------
Merge pull request #3059 from jmchilton/import_update
Fix import orders for updates to flake8_import_order.
Compare: https://github.com/galaxyproject/galaxy/compare/31cb477e1a53...4bf1994fc3fd
1
0
[galaxyproject/galaxy] a2e0e6: Initial commit for new 'Merge Collection' tool. To...
by GitHub 17 Oct '16
by GitHub 17 Oct '16
17 Oct '16
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a2e0e6ba6c404aa899a91817ccf091b9a8fcecfa
https://github.com/galaxyproject/galaxy/commit/a2e0e6ba6c404aa899a91817ccf0…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/merge_collection.xml
Log Message:
-----------
Initial commit for new 'Merge Collection' tool. Tool takes two input list collection and combined them together into a single unified list. Tool provides options on how to deal when element_identifier are found in both list
Commit: a76960b9a6523376e8d9ca6b2420d0e4883d1de0
https://github.com/galaxyproject/galaxy/commit/a76960b9a6523376e8d9ca6b2420…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
changed return statement to what it was before I forked.
Commit: d5ea4ee380c5b8ed9a536e421c7365eeb379e3a2
https://github.com/galaxyproject/galaxy/commit/d5ea4ee380c5b8ed9a536e421c73…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/style/less/ui.less
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-default.js
M static/style/blue/base.css
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into dev
Commit: a9b4d9518d1a7a7660d95a8dd312adae6ce48257
https://github.com/galaxyproject/galaxy/commit/a9b4d9518d1a7a7660d95a8dd312…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-10 (Wed, 10 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
re-worked logic to be more clear that there are three different modes when handling name conflicts
Commit: 607d10275169f54f54c6e4a9357a4bf5d05b946e
https://github.com/galaxyproject/galaxy/commit/607d10275169f54f54c6e4a9357a…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
changes based on flake8 erros
Commit: d64d278ca9c3cc766620d1f3b0659dc8a6614e9a
https://github.com/galaxyproject/galaxy/commit/d64d278ca9c3cc766620d1f3b065…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
Log Message:
-----------
Add the ability to change the suffix template to 3 different preset values. Same as Flatten collection tool. Added a test to ensure that its working.
Commit: 424acd5fcf0937b09a7be8c58e674d143d0402a8
https://github.com/galaxyproject/galaxy/commit/424acd5fcf0937b09a7be8c58e67…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
fixed flake formatting errors
Commit: c29f481dceeaaa790be1d8fdadfd58f1cb2d68c6
https://github.com/galaxyproject/galaxy/commit/c29f481dceeaaa790be1d8fdadfd…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
A lib/galaxy/tools/append_collection.xml
Log Message:
-----------
initial version of append collection tool. Allow's user to add one or more datasets to an existing collection. Provides options when we have name conflicts
Commit: b97ddd7ea52da1215c8251029f632cc972c6dba3
https://github.com/galaxyproject/galaxy/commit/b97ddd7ea52da1215c8251029f63…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M .ci/first_startup.sh
M .ci/flake8_lint_include_list.txt
M Makefile
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/library.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M config/reports.ini.sample
M config/tool_shed.ini.sample
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/dev/build_a_job_runner.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/neo4j.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/queues.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/__init__.py
A lib/galaxy/util/postfork.py
M lib/galaxy/util/template.py
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/main.js
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M run.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-repeat.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M static/style/blue/library.css
M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/tool_shed/index.mako
A test/api/test_api_batch.py
M test/base/interactor.py
A test/casperjs/api-batch-tests.js
A test/functional/tools/dbkey_output_action.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_1.xml
A test/functional/tools/tool_provided_metadata_2.xml
A test/functional/tools/tool_provided_metadata_3.xml
M test/qunit/test-data/fakeserver.js
M test/qunit/tests/form_tests.js
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
Log Message:
-----------
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into collection_tools
Commit: 5159f878cfbdaa2627be76db1d69741b3579b68f
https://github.com/galaxyproject/galaxy/commit/5159f878cfbdaa2627be76db1d69…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-26 (Fri, 26 Aug 2016)
Changed paths:
M lib/galaxy/tools/append_collection.xml
Log Message:
-----------
change tool description
Commit: f88e8a19fa270615bdfe482ca4f2d1175f56d10b
https://github.com/galaxyproject/galaxy/commit/f88e8a19fa270615bdfe482ca4f2…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/append_collection.xml
Log Message:
-----------
changed tool name and description
Commit: f54bf1bb3b0afc28d948a511001895abcaf8b15f
https://github.com/galaxyproject/galaxy/commit/f54bf1bb3b0afc28d948a5110018…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/filter_failed_collection.xml
Log Message:
-----------
Now allow filter_failed_collection to accept and filter out list:paired collection
Commit: 97ba98037992a577a9a1a6b844893f63a7339034
https://github.com/galaxyproject/galaxy/commit/97ba98037992a577a9a1a6b84489…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
now change to see if the element has dataset_instance before attempting to call it.
Commit: 4729565dfdc32482b177e3e2740f8abcbc23ab0f
https://github.com/galaxyproject/galaxy/commit/4729565dfdc32482b177e3e2740f…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
added AppendCollectionTool to list of tool_classes
Commit: 19a09e18a84a860d60e66517b3b68b58628843c7
https://github.com/galaxyproject/galaxy/commit/19a09e18a84a860d60e66517b3b6…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
R lib/galaxy/tools/append_collection.xml
Log Message:
-----------
removed append_collection tool due to John request. MergeCollection should cover all cases that append would have anyway.
Commit: ecc415369ff50dce02f5db73bdaf6fe8e60b6020
https://github.com/galaxyproject/galaxy/commit/ecc415369ff50dce02f5db73bdaf…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
Log Message:
-----------
added support to merge two list:paired collection together. Added single test to reflect new changes.
Commit: 15ad14e6620706d6dbb39176783e274e01eebb3b
https://github.com/galaxyproject/galaxy/commit/15ad14e6620706d6dbb39176783e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-16 (Sun, 16 Oct 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Enhance merge collection work from @Takadonet with more merge conflict actions.
And allow it to work over any number of input collections.
Commit: 448a27a4a1ebe2b25b40eca11b7aa319f7345c61
https://github.com/galaxyproject/galaxy/commit/448a27a4a1ebe2b25b40eca11b7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-16 (Sun, 16 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A doc/parse_gx_xsd.py
A doc/schema_template.md
M doc/source/admin/chat.rst
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/api/guidelines.rst
M doc/source/project/issues.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/dockerfiles.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
R lib/galaxy/tools/toolbox/requirements.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/filelock.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
M setup.cfg
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/tests/form_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/utility.py
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into collection_tools
Commit: 49eac93882226e6f29624c676d593ae78719d7e5
https://github.com/galaxyproject/galaxy/commit/49eac93882226e6f29624c676d59…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-16 (Sun, 16 Oct 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/merge_collection.xml
Log Message:
-----------
Cleanup merge collection and get test cases working again.
Commit: 7d938e2a23ca3ce8e3fac430bce494ce8f5238c3
https://github.com/galaxyproject/galaxy/commit/7d938e2a23ca3ce8e3fac430bce4…
Author: Philip Mabon <philipmabon(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .ci/py3_sources.txt
A .ci/validate_test_tools.sh
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
M Makefile
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A doc/parse_gx_xsd.py
A doc/schema_template.md
M doc/source/admin/chat.rst
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
A doc/source/admin/mulled_containers.rst
M doc/source/api/guidelines.rst
M doc/source/project/issues.rst
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
R lib/galaxy/datatypes/util/image_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/formatting.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/model/orm/now.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/__init__.py
M lib/galaxy/tools/cwl/cwltool_deps.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/representation.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/brew_exts.py
M lib/galaxy/tools/deps/commands.py
A lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
A lib/galaxy/tools/deps/container_resolvers/__init__.py
A lib/galaxy/tools/deps/container_resolvers/explicit.py
A lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/dockerfiles.py
A lib/galaxy/tools/deps/installable.py
A lib/galaxy/tools/deps/mulled/__init__.py
A lib/galaxy/tools/deps/mulled/_cli.py
A lib/galaxy/tools/deps/mulled/invfile.lua
A lib/galaxy/tools/deps/mulled/mulled_build.py
A lib/galaxy/tools/deps/mulled/mulled_build_channel.py
A lib/galaxy/tools/deps/mulled/mulled_build_files.py
A lib/galaxy/tools/deps/mulled/mulled_build_tool.py
A lib/galaxy/tools/deps/mulled/mulled_search.py
A lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/exception_handling.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/__init__.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
R lib/galaxy/tools/toolbox/requirements.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/asserts/xml.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
A lib/galaxy/tools/xsd/LICENSE
A lib/galaxy/tools/xsd/README.md
A lib/galaxy/tools/xsd/galaxy.jxb
A lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
A lib/galaxy/util/filelock.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
A lib/galaxy/util/image_util.py
M lib/galaxy/util/json.py
M lib/galaxy/util/lazy_process.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/pastescript/serve.py
M lib/galaxy/util/permutations.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/sockets.py
M lib/galaxy/util/sqlite.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/topsort.py
M lib/galaxy/util/validation.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
R lib/galaxy/web/proxy/filelock.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/genomes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/galaxy_install/tools/data_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
A scripts/validate_tools.sh
M setup.cfg
M static/maps/layout/menu.js.map
M static/maps/layout/scratchbook.js.map
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/layout/scratchbook.js
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
M templates/admin/tool_shed_repository/common.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/show_params.mako
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/galaxy/workflow/run.mako
R templates/webapps/galaxy/workflow/run_complete.mako
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/helpers.py
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_users.py
A test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/workflows_format_2/__init__.py
M test/api/workflows_format_2/converter.py
M test/api/workflows_format_2/main.py
M test/base/api.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/test_logging.py
M test/base/twilltestcase.py
M test/functional/test_data_managers.py
M test/functional/test_library_templates.py
M test/functional/test_toolbox.py
A test/functional/tools/color_param.xml
M test/functional/tools/column_multi_param.xml
M test/functional/tools/column_param.xml
M test/functional/tools/identifier_collection.xml
M test/functional/tools/identifier_multiple.xml
M test/functional/tools/identifier_single.xml
M test/functional/tools/inputs_as_json.xml
A test/functional/tools/metadata_column_names.xml
A test/functional/tools/mulled_example_multi_1.xml
A test/functional/tools/multi_data_optional.xml
M test/functional/tools/multi_output.xml
M test/functional/tools/multi_output_assign_primary.xml
M test/functional/tools/multi_output_configured.xml
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_directory.xml
M test/functional/tools/validation_repeat.xml
M test/functional/workflow.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/tests/form_tests.js
M test/shed_functional/base/test_db_util.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_objectstore.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/utility.py
M test/unit/workflows/test_run_parameters.py
M tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge pull request #1 from jmchilton/collection_tools
Enhance the Merge Collections Tool
Commit: 31cb477e1a538c74360f039dda23907d0856adb6
https://github.com/galaxyproject/galaxy/commit/31cb477e1a538c74360f039dda23…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-17 (Mon, 17 Oct 2016)
Changed paths:
M config/tool_conf.xml.sample
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/filter_failed_collection.xml
A lib/galaxy/tools/merge_collection.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #2771 from Takadonet/dev
Collection Operator tools
Compare: https://github.com/galaxyproject/galaxy/compare/a895c823daaf...31cb477e1a53
1
0