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
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
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
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
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