Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b9e4bf58c5b656089ac8402632677503e6a86c65
https://github.com/galaxyproject/galaxy/commit/b9e4bf58c5b656089ac840263267…
Author: Lance Parsons <lparsons(a)princeton.edu>
Date: 2016-10-13 (Thu, 13 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
Log Message:
-----------
Sort bedtools output in bam_to_bigwig conversion
Bedtools genomecov seems to output bedgraph files with chromosomes
sorted in the order given in the chromInfo file. This can cause issues
with bedGraphToBigWig which requires them sorted in a specific way.
Fixes #2582.
Commit: 9e1331f1b37a40d8894fc724bb745589bc5e213b
https://github.com/galaxyproject/galaxy/commit/9e1331f1b37a40d8894fc724bb74…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
Log Message:
-----------
Merge pull request #3049 from lparsons/bam_to_bigwig
Sort bedtools output in bam_to_bigwig conversion
Compare: https://github.com/galaxyproject/galaxy/compare/25527bec32b2...9e1331f1b37a
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d9dfc2cc78339f9b2158a07fff3df0a24d081865
https://github.com/galaxyproject/galaxy/commit/d9dfc2cc78339f9b2158a07fff3d…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
A static/maps/mvc/ui/ui-thumbnails.js.map
A static/scripts/mvc/ui/ui-thumbnails.js
M static/style/blue/base.css
Log Message:
-----------
Move thumbnail list view to shared ui elements
Commit: 296ef7e232468a2311ba18763752d97e10c63a2d
https://github.com/galaxyproject/galaxy/commit/296ef7e232468a2311ba18763752…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M static/maps/mvc/ui/ui-tabs.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
Log Message:
-----------
Hide tabs navigation if there is only one tab
Commit: aab59be19160a97f41c60b7dab741825c90be934
https://github.com/galaxyproject/galaxy/commit/aab59be19160a97f41c60b7dab74…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/style/less/ui.less
M static/style/blue/base.css
Log Message:
-----------
Fix margin
Commit: ec9ca3ffd1bcb2a6e70a5a1f2c8e0183e80ddc1a
https://github.com/galaxyproject/galaxy/commit/ec9ca3ffd1bcb2a6e70a5a1f2c8e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M config/plugins/visualizations/charts/static/client/views/editor.js
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/mvc/ui/ui-thumbnails.js
Log Message:
-----------
Fix list view title
Commit: 0b1c171ebc2b9b0605a6ef1e8e5b68e20d579c74
https://github.com/galaxyproject/galaxy/commit/0b1c171ebc2b9b0605a6ef1e8e5b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M config/plugins/visualizations/charts/static/client/views/editor.js
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Revise tab viewer, add test cases
Commit: c4526bdaba29ccc9b045dea429dbc0c3fa0e5b15
https://github.com/galaxyproject/galaxy/commit/c4526bdaba29ccc9b045dea429db…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M static/maps/mvc/ui/ui-tabs.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
Log Message:
-----------
Hide tab navbar if there is only one tab available
Commit: 25527bec32b2431f1a8769ef79f34ad9af38c0db
https://github.com/galaxyproject/galaxy/commit/25527bec32b2431f1a8769ef79f3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/style/less/ui.less
M config/plugins/visualizations/charts/static/client/app.css
M config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/types.js
M static/maps/mvc/ui/ui-tabs.js.map
A static/maps/mvc/ui/ui-thumbnails.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-tabs.js
A static/scripts/mvc/ui/ui-thumbnails.js
M static/style/blue/base.css
M test/qunit/tests/ui_tests.js
Log Message:
-----------
Merge pull request #3079 from guerler/reusable_grid_view
Move thumbnail list view to shared ui elements, revise tabs, add test cases
Compare: https://github.com/galaxyproject/galaxy/compare/f9ee0f86376f...25527bec32b2
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4bfac4536971c54a704c76de083de0600332442c
https://github.com/galaxyproject/galaxy/commit/4bfac4536971c54a704c76de083d…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M doc/patch.py
Log Message:
-----------
Fix flake8 errors and Python3 compatibility for doc/patch.py
Commit: a21ed34efb695fb71f1c7616dc1655de8b54be41
https://github.com/galaxyproject/galaxy/commit/a21ed34efb695fb71f1c7616dc16…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
R doc/source/admin/interactive_environments_success.png
A doc/source/dev/interactive_environments_success.png
Log Message:
-----------
Move png in the right directory
Broken in #2543.
Commit: 8a17143bc77ce370974e35f51d699f8029edd647
https://github.com/galaxyproject/galaxy/commit/8a17143bc77ce370974e35f51d69…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
R doc/source/lib/galaxy.util.backports.importlib.rst
R scripts/bootstrap_history_announce_template.rst
Log Message:
-----------
Remove unused files
Commit: e6d0b69ec89786f56fa71d2e893b2361bbe55d0e
https://github.com/galaxyproject/galaxy/commit/e6d0b69ec89786f56fa71d2e893b…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M doc/source/dev/build_a_job_runner.rst
A doc/source/dev/inherit.png
A doc/source/dev/queue.png
A doc/source/dev/queue_b.png
A doc/source/dev/runner_diag.png
Log Message:
-----------
Add and use local images for build runner doc
Commit: 3180b631662ced589fe9db42d27caa58638b5f8d
https://github.com/galaxyproject/galaxy/commit/3180b631662ced589fe9db42d27c…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M .gitignore
M Makefile
M doc/Makefile
M doc/parse_gx_xsd.py
M doc/schema_template.md
M doc/source/dev/index.rst
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Properly integrate tool XML schema with docs
Generate intermediate rst file instead of html
Move generation to doc/Makefile
Use pandoc to generate table of contents and fragment ids.
Remove nested inline markup (not supported by reStructuredText)
Fix https and other links.
Commit: 527e332aa39e82224965e6aaef94ffaa1cf956bf
https://github.com/galaxyproject/galaxy/commit/527e332aa39e82224965e6aaef94…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-10-24 (Mon, 24 Oct 2016)
Changed paths:
M doc/source/admin/conda_faq.rst
M doc/source/admin/interactive_environments.rst
M doc/source/admin/mulled_containers.rst
M doc/source/conf.py
M doc/source/index.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.rst
M doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07.rst
M doc/source/releases/index.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/managers/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/util/simplegraph.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/bootstrap_history.py
M scripts/galaxy-main
Log Message:
-----------
Fix a bunch of errors reported by Sphinx
Commit: f9ee0f86376f90ede636e4874cca120d30e7cd8c
https://github.com/galaxyproject/galaxy/commit/f9ee0f86376f90ede636e4874cca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-10-31 (Mon, 31 Oct 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M Makefile
M doc/Makefile
M doc/parse_gx_xsd.py
M doc/patch.py
M doc/schema_template.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments_success.png
M doc/source/admin/mulled_containers.rst
M doc/source/conf.py
M doc/source/dev/build_a_job_runner.rst
M doc/source/dev/index.rst
A doc/source/dev/inherit.png
A doc/source/dev/interactive_environments_success.png
A doc/source/dev/queue.png
A doc/source/dev/queue_b.png
A doc/source/dev/runner_diag.png
M doc/source/index.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.tools.linters.rst
M doc/source/lib/galaxy.tools.parameters.rst
R doc/source/lib/galaxy.util.backports.importlib.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.rst
M doc/source/releases/16.04.rst
M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07.rst
M doc/source/releases/index.rst
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/checkers.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/__init__.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/managers/__init__.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/simplegraph.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M scripts/bootstrap_history.py
R scripts/bootstrap_history_announce_template.rst
M scripts/galaxy-main
Log Message:
-----------
Merge pull request #3086 from nsoranzo/fix_doc
Properly integrate tool XML schema with docs
Compare: https://github.com/galaxyproject/galaxy/compare/f0c5d5ca39d1...f9ee0f86376f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6e4f3d9d2d1a01b539d412aad5bb8fbe0ba95a17
https://github.com/galaxyproject/galaxy/commit/6e4f3d9d2d1a01b539d412aad5bb…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Revert menu.js, tool-form.js to pre-webhooks-PR
Commit: 62773a72c728b8bab46804d2128e46f62d45cd1d
https://github.com/galaxyproject/galaxy/commit/62773a72c728b8bab46804d2128e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Reapply isolated menu.js webhook changes
Commit: 67b1d45e3657af077005ed7b0b1469a7fd3f42d0
https://github.com/galaxyproject/galaxy/commit/67b1d45e3657af077005ed7b0b14…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Reapply isolated tool-form.js webhook changes
Commit: 2458c5455fe07c7832cb30fd5bdedc9770db6f42
https://github.com/galaxyproject/galaxy/commit/2458c5455fe07c7832cb30fd5bde…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-10-27 (Thu, 27 Oct 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M static/maps/layout/menu.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #3102 from dannon/fix_webhook_js_merge
Fixes for remaining webhooks PR issues.
Compare: https://github.com/galaxyproject/galaxy/compare/660d70f8b4da...2458c5455fe0