Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: aa85760996fa6d6dd9b94a38cf7220d39b8770bc
https://github.com/galaxyproject/galaxy/commit/aa85760996fa6d6dd9b94a38cf72…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-05-18 (Thu, 18 May 2017)
Changed paths:
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Rebuild to provide new localization.
Commit: e826ded26415ef29257acce776d02d272994a25c
https://github.com/galaxyproject/galaxy/commit/e826ded26415ef29257acce776d0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-18 (Thu, 18 May 2017)
Changed paths:
M static/maps/nls/fr/locale.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js.map
M static/scripts/nls/fr/locale.js
Log Message:
-----------
Merge pull request #4081 from dannon/locale_rebuild
Rebuild to provide new localization.
Compare: https://github.com/galaxyproject/galaxy/compare/e09aabe1d504...e826ded26415
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 2099c09f6ab5a8f5951d01cd6fa67681618e2dda
https://github.com/galaxyproject/galaxy/commit/2099c09f6ab5a8f5951d01cd6fa6…
Author: Thodoris Sotiropoulos <theosot(a)grnet.gr>
Date: 2017-04-20 (Thu, 20 Apr 2017)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/jobs/runners/chronos.py
Log Message:
-----------
Add job runner for Chronos
Chronos is a framework for the Apache Mesos; a software which manages
computer clusters. Specifically, Chronos is a batch processing
scheduler that runs on top of Mesos and it is used for job
orchestration.
Commit: 339c3724fb94d7d85732c7ef7f8f48e822f83c7d
https://github.com/galaxyproject/galaxy/commit/339c3724fb94d7d85732c7ef7f8f…
Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr>
Date: 2017-04-26 (Wed, 26 Apr 2017)
Changed paths:
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Add chronos client to the pinned-requirements.txt
Commit: 05ee848cd327ab293e20300d22dae94fc0e0473e
https://github.com/galaxyproject/galaxy/commit/05ee848cd327ab293e20300d22da…
Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Pin version of chronos-python to 0.38
Commit: c01c9bbe616c9524883db148df38e770ea25547e
https://github.com/galaxyproject/galaxy/commit/c01c9bbe616c9524883db148df38…
Author: Thodoris Sotiropoulos <theosot(a)dmst.aueb.gr>
Date: 2017-05-05 (Fri, 05 May 2017)
Changed paths:
M config/job_conf.xml.sample_advanced
Log Message:
-----------
Add an explanatory comment about job_conf of chronos
Commit: 7028ca04c7554e87ca7ad63a547d962476810080
https://github.com/galaxyproject/galaxy/commit/7028ca04c7554e87ca7ad63a547d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-18 (Thu, 18 May 2017)
Changed paths:
M config/job_conf.xml.sample_advanced
M lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/jobs/runners/chronos.py
Log Message:
-----------
Merge pull request #3946 from theosotr/feature-chronos
Add job runner for Chronos
Compare: https://github.com/galaxyproject/galaxy/compare/b9fb2de42b53...7028ca04c755
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f8e92fe011b17c8a2f3b249453043854a1cff305
https://github.com/galaxyproject/galaxy/commit/f8e92fe011b17c8a2f3b24945304…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-17 (Wed, 17 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Add parameter to workflows API to list workflows with missing tools.
Commit: ddbbe76c0a8266d4c49694ef43d43ecefb2ac943
https://github.com/galaxyproject/galaxy/commit/ddbbe76c0a8266d4c49694ef43d4…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-18 (Thu, 18 Aug 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/model/__init__.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/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/template.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/webapps/galaxy/api/history_contents.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/controllers/repository.py
M lib/galaxy_ext/metadata/set_metadata.py
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 test/base/interactor.py
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
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 24bc782259786c03b0279e5e33b2eb96c1933c89
https://github.com/galaxyproject/galaxy/commit/24bc782259786c03b0279e5e33b2…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-18 (Thu, 18 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Implement display of workflows missing tools and the repository that contains those tools.
Commit: e8255841573b551c36e444e1559f8665687d3b9d
https://github.com/galaxyproject/galaxy/commit/e8255841573b551c36e444e1559f…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-19 (Fri, 19 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/model/migrate/check.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: ec153e30627ad46a091a1a24a494cc2314ce22b1
https://github.com/galaxyproject/galaxy/commit/ec153e30627ad46a091a1a24a494…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-19 (Fri, 19 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Allow adding a repository to the queue from a workflow.
Commit: f72f1f106c161d3d4d87dc0670b92a7f42b0207c
https://github.com/galaxyproject/galaxy/commit/f72f1f106c161d3d4d87dc0670b9…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
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
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 4a02d0516ff7c661ad9b46dcd428ccdc8cba3717
https://github.com/galaxyproject/galaxy/commit/4a02d0516ff7c661ad9b46dcd428…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-22 (Mon, 22 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Move the method that checks for missing tools into the toolbox, where it belongs.
Commit: ca987e706fb0a128fc3d68ea6f07f3fd44e83d74
https://github.com/galaxyproject/galaxy/commit/ca987e706fb0a128fc3d68ea6f07…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/scripts/mvc/dataset/data.js
M config/galaxy.ini.sample
M config/reports.ini.sample
M config/tool_shed.ini.sample
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/util/postfork.py
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M static/maps/mvc/dataset/data.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 templates/webapps/tool_shed/index.mako
A test/api/test_api_batch.py
A test/casperjs/api-batch-tests.js
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 73cdfc716bba938921d1fd9262b25a6778cc7f10
https://github.com/galaxyproject/galaxy/commit/73cdfc716bba938921d1fd9262b2…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.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_toolshed.py
Log Message:
-----------
Rework the return value of /api/workflows?missing_tools=True
Commit: 57c01f11af470e62164566af2b4af609d1cbebb9
https://github.com/galaxyproject/galaxy/commit/57c01f11af470e62164566af2b4a…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-25 (Thu, 25 Aug 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Update the display of workflows missing tools.
Thus accomodating the API changes made in the previous commit.
Commit: 4d85eec0c9b8dda5d971aaf8714e65886f7e2f41
https://github.com/galaxyproject/galaxy/commit/4d85eec0c9b8dda5d971aaf8714e…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M Makefile
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
M doc/source/releases/16.07.rst
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M scripts/bootstrap_history.py
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 5b65f122b3808232656f0b8730cf46a697eb26d2
https://github.com/galaxyproject/galaxy/commit/5b65f122b3808232656f0b8730cf…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-29 (Mon, 29 Aug 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Finish repository discovery by missing workflow tools.
Commit: d9d3f259944b640f2844745c895224f8bb9ea6bd
https://github.com/galaxyproject/galaxy/commit/d9d3f259944b640f2844745c8952…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M doc/source/admin/chat.rst
M doc/source/admin/conda_faq.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M templates/webapps/galaxy/workflow/display.mako
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: de1510f3cc367c036bf6c19bcd15e95f5dc46b30
https://github.com/galaxyproject/galaxy/commit/de1510f3cc367c036bf6c19bcd15…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-08-30 (Tue, 30 Aug 2016)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Fix the imports I broke in an earlier commit.
Commit: 6e40fe957a777c6b64218844bc521da946f65279
https://github.com/galaxyproject/galaxy/commit/6e40fe957a777c6b64218844bc52…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-02 (Fri, 02 Sep 2016)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M 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/maps/layout/scratchbook.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
M templates/admin/tool_shed_repository/common.mako
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 6998d338cfa22644d1fdc2cec819ee504147e784
https://github.com/galaxyproject/galaxy/commit/6998d338cfa22644d1fdc2cec819…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-12 (Mon, 12 Sep 2016)
Changed paths:
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/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/tool_shed/util/repository_util.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Integrate whoosh with the API installation's search boxes.
Commit: aae40ca9064a67e57b12b30837f96de14bd5a4a9
https://github.com/galaxyproject/galaxy/commit/aae40ca9064a67e57b12b30837f9…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-12 (Mon, 12 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/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/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/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/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' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 0baf22ca6f891497a265fcefd3141a0796e1fd5d
https://github.com/galaxyproject/galaxy/commit/0baf22ca6f891497a265fcefd314…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-13 (Tue, 13 Sep 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
A lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M templates/show_params.mako
M test/unit/jobs/test_job_wrapper.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 0e1a2291ee77e710e908a7734eee20c43016f12c
https://github.com/galaxyproject/galaxy/commit/0e1a2291ee77e710e908a7734eee…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-19 (Mon, 19 Sep 2016)
Changed paths:
A .ci/validate_test_tools.sh
M .travis.yml
M CONTRIBUTORS.md
M LICENSE.txt
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
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/tools/parameters/validation.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/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.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
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M templates/webapps/galaxy/workflow/run.mako
R test/functional/tools/multi_page.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/managers/test_DatasetManager.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 4106d975fa5b8767d72b13671ce183d9a8bd98ad
https://github.com/galaxyproject/galaxy/commit/4106d975fa5b8767d72b13671ce1…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-19 (Mon, 19 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Some cleanup, initial url hash navigation.
Commit: cdea4b3cee3024618e99b6b1f498d2f25fa53295
https://github.com/galaxyproject/galaxy/commit/cdea4b3cee3024618e99b6b1f498…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 8d15670a5d4709cf9043ffd0d3b296494fc252fb
https://github.com/galaxyproject/galaxy/commit/8d15670a5d4709cf9043ffd0d3b2…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Remove debugging.
Commit: 22240074c30a98c541c36b6dab4fb0947112b6be
https://github.com/galaxyproject/galaxy/commit/22240074c30a98c541c36b6dab4f…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Initial work to show tool form preview on repository preview page.
Commit: ca7fb1db62e6c1f03bfc0836f1bd7aeacb1f0294
https://github.com/galaxyproject/galaxy/commit/ca7fb1db62e6c1f03bfc0836f1bd…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/tool_shed/api/tools.py
Log Message:
-----------
Make request_context (trans) the first argument to populate_model.
Commit: 18b93014572c04d597b9ea6f0750686e9cba39b4
https://github.com/galaxyproject/galaxy/commit/18b93014572c04d597b9ea6f0750…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-20 (Tue, 20 Sep 2016)
Changed paths:
M lib/galaxy/web/framework/decorators.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 07cc3a9462db302478ab4aacd378b6128282e52b
https://github.com/galaxyproject/galaxy/commit/07cc3a9462db302478ab4aacd378…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/extract.py
M templates/user/info.mako
M templates/user/register.mako
M templates/user/username.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
M test/unit/managers/test_UserManager.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 5309c8eeb782140fa7f729d7933a388cf29f6505
https://github.com/galaxyproject/galaxy/commit/5309c8eeb782140fa7f729d7933a…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Show a modal with the tool form when clicking on the button.
Commit: dd783f418e3fb33a169766235febffa575e0696a
https://github.com/galaxyproject/galaxy/commit/dd783f418e3fb33a169766235feb…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
A bit of styling.
Commit: 6da7ce304e34db2cb0495cdd88c553514514573b
https://github.com/galaxyproject/galaxy/commit/6da7ce304e34db2cb0495cdd88c5…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Additional styling.
Commit: d60bc8a97b5f229bbf9416e4e5a0f92e028aad01
https://github.com/galaxyproject/galaxy/commit/d60bc8a97b5f229bbf9416e4e5a0…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-21 (Wed, 21 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/tools.py
Log Message:
-----------
Improve travis' demeanor.
Commit: b29d6f55d8546aac4354d4293ee585d08645c790
https://github.com/galaxyproject/galaxy/commit/b29d6f55d8546aac4354d4293ee5…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-09-23 (Fri, 23 Sep 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/tools.py
Log Message:
-----------
Remove unused import.
Commit: adbcc26286909bae7bd0a9c4587ea4815137a8e3
https://github.com/galaxyproject/galaxy/commit/adbcc26286909bae7bd0a9c4587e…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-09-26 (Mon, 26 Sep 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Fix the per-tool panel selection features.
Commit: ea9f22ebf794be55b5c89090acf51b9f0040b582
https://github.com/galaxyproject/galaxy/commit/ea9f22ebf794be55b5c89090acf5…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M Makefile
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
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
M lib/galaxy/datatypes/data.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/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/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/slurm.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/mapping.py
M lib/galaxy/queue_worker.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/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/checkers.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/library_common.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/tool_shed/util/metadata_util.py
M scripts/bootstrap_history.py
M scripts/tool_shed/build_ts_whoosh_index.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/utils/utils.js
M static/style/blue/base.css
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/library/common/common.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
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/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 tools/data_source/data_source.py
M tools/data_source/hbvar_filter.py
M tools/data_source/microbial_import_code.py
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/filters/axt_to_concat_fasta.py
M tools/filters/axt_to_fasta.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sff_extract.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 92724347feedac97f319af6c8ab6f2c703ef9811
https://github.com/galaxyproject/galaxy/commit/92724347feedac97f319af6c8ab6…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Fix repository installation.
Commit: 84545674af6fc81e0f5a2dd87448aaee176106eb
https://github.com/galaxyproject/galaxy/commit/84545674af6fc81e0f5a2dd87448…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-10-04 (Tue, 04 Oct 2016)
Changed paths:
M templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Fix the 'Add from workflow' button.
Commit: 60b12bf6734b460881e28a257b5d28301129785d
https://github.com/galaxyproject/galaxy/commit/60b12bf6734b460881e28a257b5d…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
A .ci/flake8_docstrings_include_list.txt
M .ci/flake8_wrapper.sh
A .ci/flake8_wrapper_docstrings.sh
M .travis.yml
M 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 doc/source/admin/conda_faq.rst
M doc/source/api/guidelines.rst
M lib/galaxy/managers/workflows.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/meta.py
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 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/unit/workflows/test_run_parameters.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 02719c6547e91cc1357ad6ed49e97096c46f5473
https://github.com/galaxyproject/galaxy/commit/02719c6547e91cc1357ad6ed49e9…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-10-07 (Fri, 07 Oct 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Remove unused imports.
Commit: 815a713226c72f3d063ba7f1bf2e0f721dc2407d
https://github.com/galaxyproject/galaxy/commit/815a713226c72f3d063ba7f1bf2e…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-09 (Wed, 09 Nov 2016)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CONTRIBUTORS.md
M Makefile
M client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
A client/galaxy/scripts/mvc/ui/ui-thumbnails.js
A client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
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
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R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
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R config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
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M test/unit/jobs/test_runner_local.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_toolbox.py
M test/unit/tools_support.py
M test/unit/unittest_utils/utility.py
A tool-data/blastdb.loc.sample
A tool-data/blastdb_d.loc.sample
A tool-data/blastdb_p.loc.sample
M tools/data_source/upload.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/stats/filtering.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into repo_queue_sharing
Commit: 9e37adb93251ea72e6592966e6b5e810a756f9d8
https://github.com/galaxyproject/galaxy/commit/9e37adb93251ea72e6592966e6b5…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-09 (Wed, 09 Nov 2016)
Changed paths:
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/mvc/toolshed/categories-view.js
A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-view.js
A client/galaxy/scripts/mvc/toolshed/shed-list-view.js
A client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
A static/maps/admin.toolshed.js.map
A static/maps/mvc/toolshed/repo-queue-view.js.map
A static/maps/mvc/toolshed/shed-category-view.js.map
A static/maps/mvc/toolshed/shed-repo-details-view.js.map
A static/maps/mvc/toolshed/shed-repo-list-view.js.map
A static/maps/mvc/toolshed/sheds-list-view.js.map
A static/maps/mvc/toolshed/toolshed-model.js.map
A static/scripts/admin.toolshed.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
A static/scripts/mvc/toolshed/categories-view.js
A static/scripts/mvc/toolshed/repo-queue-view.js
A static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-view.js
A static/scripts/mvc/toolshed/shed-category-view.js
A static/scripts/mvc/toolshed/shed-list-view.js
A static/scripts/mvc/toolshed/shed-repo-details-view.js
A static/scripts/mvc/toolshed/shed-repo-list-view.js
A static/scripts/mvc/toolshed/sheds-list-view.js
A static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/webhooks.js
R templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Initial backbonification of API repo installation.
Commit: 1700b1f3a5ebf72fdacafcf067cba23e3a88db1a
https://github.com/galaxyproject/galaxy/commit/1700b1f3a5ebf72fdacafcf067cb…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-10 (Thu, 10 Nov 2016)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/admin.toolshed.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix forward navigation.
Commit: 1e8965f1e4f68c4bec8c9bc832bb55330e3942a5
https://github.com/galaxyproject/galaxy/commit/1e8965f1e4f68c4bec8c9bc832bb…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix installation.
Commit: 476df39fe2163a00bbcd441e66f49b14325bf3af
https://github.com/galaxyproject/galaxy/commit/476df39fe2163a00bbcd441e66f4…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-11 (Fri, 11 Nov 2016)
Changed paths:
M lib/galaxy/model/mapping.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/tool_shed/tools/tool_validator.py
M scripts/api/filter_failed_datasets_from_collection.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: 104aee5114880d744f427dcd96515d193d3798f0
https://github.com/galaxyproject/galaxy/commit/104aee5114880d744f427dcd9651…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Some cleanup, improved the jstree.
Commit: 529c7c5b74470f8a1dfb8a913ca0e84d55f8610d
https://github.com/galaxyproject/galaxy/commit/529c7c5b74470f8a1dfb8a913ca0…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix tool form modal.
Commit: edd7417102e51bde3ae199365b05c519cd0d6f3b
https://github.com/galaxyproject/galaxy/commit/edd7417102e51bde3ae199365b05…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M Makefile
M config/galaxy.ini.sample
M doc/source/admin/interactive_environments.rst
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/model/__init__.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/cwl/runtime_actions.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/_cli.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/imp_exp/exp_history_to_archive.xml
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/toolbox/lineages/tool_shed.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: 419fb3bde91d792bbda6f2a291c99371cad96d29
https://github.com/galaxyproject/galaxy/commit/419fb3bde91d792bbda6f2a291c9…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-14 (Mon, 14 Nov 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
A lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Refactor API endpoints.
Commit: d00f89707f591b226b1d501959e648a45f62431b
https://github.com/galaxyproject/galaxy/commit/d00f89707f591b226b1d501959e6…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-15 (Tue, 15 Nov 2016)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M lib/galaxy/webapps/galaxy/api/toolshed.py
M static/scripts/admin.toolshed.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
Log Message:
-----------
Fix navigation, update API calls.
Commit: 3e83e5ba811bbac19864b39f632f294956c7587e
https://github.com/galaxyproject/galaxy/commit/3e83e5ba811bbac19864b39f632f…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix disabling button when changeset is installed.
Commit: 8ead327a46b0dfcde163e4591895f41575fac21f
https://github.com/galaxyproject/galaxy/commit/8ead327a46b0dfcde163e4591895…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2016-11-16 (Wed, 16 Nov 2016)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
Log Message:
-----------
Tweaked the UI a bit.
Commit: 9463d94a2aa4d30140d18094db55bb4e58e9ebc7
https://github.com/galaxyproject/galaxy/commit/9463d94a2aa4d30140d18094db55…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-01-06 (Fri, 06 Jan 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
A .ci/jenkins/api/run_tests.sh
A .ci/jenkins/framework/run_tests.sh
A .ci/jenkins/integration/run_tests.sh
A .ci/jenkins/selenium/Dockerfile
A .ci/jenkins/selenium/docker-compose.yml
A .ci/jenkins/selenium/galaxy.ini
A .ci/jenkins/selenium/run_galaxy.bash
A .ci/jenkins/selenium/run_tests.sh
A .ci/jenkins/toolshed/run_tests.sh
M .ci/py3_sources.txt
M Makefile
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
A client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/source_material/circle.py
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.xml
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/webpack.config.js
M contrib/galaxy_config_merger.py
M contrib/nagios/check_galaxy.py
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
A display_applications/igv/genome_fasta.xml
M doc/Makefile
A doc/fix_schema_rst.sh
M doc/parse_gx_xsd.py
M doc/patch.py
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/index.rst
M doc/source/admin/interactive_environments.rst
M doc/source/admin/interactive_environments.svg
M doc/source/admin/webhooks.rst
M doc/source/dev/faq.rst
M doc/source/dev/interactive_environments.rst
M doc/source/project/organization.rst
A doc/source/releases/16.10.rst
M doc/source/releases/16.10_announce.rst
A doc/source/releases/17.01_announce.rst
M lib/galaxy/actions/admin.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
M lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
A lib/galaxy/datatypes/converters/fasta_to_fai.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
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M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
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M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
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M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
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M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/neo4j.py
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M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/1.smat
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M lib/galaxy/dependencies/pinned-requirements.txt
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M lib/galaxy/external_services/parameters.py
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A lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
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M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
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M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
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M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
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M lib/galaxy/sample_tracking/request_types.py
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M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_transactions.py
M test/unit/test_routes.py
M test/unit/test_sockets.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_external_files.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/upload.py
M tools/evolution/add_scores.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_fasta.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
R tools/filters/gff/sort_gtf.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/lav_to_bed.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/uniq.py
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_file_browser.py
M tools/genomespace/genomespace_importer.py
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/phenotype_association/pagetag.py
M tools/phenotype_association/senatag.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
Log Message:
-----------
Merge in -dev.
Commit: 6954c082fded87b9ab71f97675aa7bc94a975770
https://github.com/galaxyproject/galaxy/commit/6954c082fded87b9ab71f97675aa…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-01-06 (Fri, 06 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
A client/galaxy/scripts/mvc/toolshed/util.js
M lib/galaxy/webapps/galaxy/api/toolshed.py
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
Log Message:
-----------
Preliminary commit before fixing the search autocomplete.
Commit: c955e6fd979a9a402b57f083930108146b21f24a
https://github.com/galaxyproject/galaxy/commit/c955e6fd979a9a402b57f0839301…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-01-12 (Thu, 12 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
Log Message:
-----------
Fix searching.
Commit: de8e43fd65d001a2a076ea4044d192199ae3c446
https://github.com/galaxyproject/galaxy/commit/de8e43fd65d001a2a076ea4044d1…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-01-19 (Thu, 19 Jan 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix tool form modal.
Commit: 8d5b154ef0d25e4b8cbbba7128d14c26e2c4a758
https://github.com/galaxyproject/galaxy/commit/8d5b154ef0d25e4b8cbbba7128d1…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-02 (Thu, 02 Feb 2017)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M static/maps/admin.toolshed.js.map
M static/maps/mvc/toolshed/toolshed-model.js.map
M static/scripts/admin.toolshed.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
Log Message:
-----------
Finally got the repository queue rendering semi-properly.
Commit: e92fcf1457e0396e3173b1b7541c53b26a33a47b
https://github.com/galaxyproject/galaxy/commit/e92fcf1457e0396e3173b1b7541c…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-03 (Fri, 03 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/run_galaxy.bash
M .ci/py3_sources.txt
M README.rst
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-misc.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/style/less/base.less
A config/build_sites.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/csg/templates/csg.mako
M config/plugins/visualizations/graphviz/templates/graphviz.mako
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
R config/plugins/webhooks/demo/history_test1/config/history_test1.yml
R config/plugins/webhooks/demo/history_test2/config/history_test2.yml
R config/plugins/webhooks/demo/masthead_test/config/masthead_test.yml
R config/plugins/webhooks/demo/phdcomics/config/phdcomics.yaml
R config/plugins/webhooks/demo/phdcomics/helper/__init__.py
R config/plugins/webhooks/demo/phdcomics/static/script.js
R config/plugins/webhooks/demo/phdcomics/static/styles.css
R config/plugins/webhooks/demo/trans_object/config/trans_object.yaml
R config/plugins/webhooks/demo/trans_object/helper/__init__.py
R config/plugins/webhooks/demo/xkcd/config/xkcd.yml
R config/plugins/webhooks/demo/xkcd/static/script.js
R config/plugins/webhooks/demo/xkcd/static/styles.css
M doc/schema_template.md
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/webhooks.rst
M doc/source/api/guidelines.rst
M doc/source/project/organization.rst
M lib/galaxy/auth/providers/__init__.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/types/__init__.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml
A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml
A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml
A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml
A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml
A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml
A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml
A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml
A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml
A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/diamond_db.dmnd
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/job/__init__.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/shell/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/jobs/runners/util/condor/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/runners/util/retry.py
M lib/galaxy/jobs/runners/util/sudo.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.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/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/dependencies.py
M lib/galaxy/tools/deps/installable.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
A lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
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/views.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/export_history.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/filters/examples.py.sample
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/tags.py
M lib/galaxy/tools/util/galaxyops/__init__.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.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/tools/xsd/galaxy.xsd
A lib/galaxy/util/compression_utils.py
M lib/galaxy/util/json.py
M lib/galaxy/util/object_wrapper.py
A lib/galaxy/util/oset.py
M lib/galaxy/util/properties.py
M lib/galaxy/version.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webhooks/__init__.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/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy/workflow/steps.py
M lib/galaxy_utils/sequence/sequence.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/workflow_util.py
M run.sh
M run_tests.sh
M scripts/bootstrap_history.py
M scripts/common_startup.sh
A scripts/manage_tool_dependencies.py
A static/maps/libs/showdown.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-misc.js.map
M static/maps/mvc/workflow/workflow-canvas.js.map
A static/maps/mvc/workflow/workflow-icons.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/mvc/workflow/workflow-view.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.map
A static/scripts/libs/showdown.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-misc.js
M static/scripts/mvc/workflow/workflow-canvas.js
A static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/viz/trackster/tracks.js
M static/style/blue/base.css
M templates/ind_share_base.mako
M templates/webapps/galaxy/history/share.mako
R templates/webapps/galaxy/workflow/editor_generic_form.mako
R templates/webapps/galaxy/workflow/editor_tool_form.mako
A test-data/1.fastqsanger.bz2
A test-data/1.fastqsanger.gz
A test-data/simple.xml
R test/api/helpers.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_search.py
M test/api/test_tools.py
A test/api/test_visualizations.py
A test/api/test_webhooks.py
R test/api/test_workflow_1.ga
R test/api/test_workflow_2.ga
R test/api/test_workflow_batch.ga
M test/api/test_workflow_extraction.py
R test/api/test_workflow_map_reduce_pause.ga
R test/api/test_workflow_matching_lists.ga
R test/api/test_workflow_missing_tool.ga
R test/api/test_workflow_pause.ga
R test/api/test_workflow_topoambigouity.ga
R test/api/test_workflow_topoambigouity_auto_laidout.ga
R test/api/test_workflow_validation_1.ga
R test/api/test_workflow_with_runtime_input.ga
M test/api/test_workflows.py
R test/api/workflows_format_2/README.txt
R test/api/workflows_format_2/__init__.py
R test/api/workflows_format_2/converter.py
R test/api/workflows_format_2/interface.py
R test/api/workflows_format_2/main.py
A test/base/data/test_workflow_1.ga
A test/base/data/test_workflow_2.ga
A test/base/data/test_workflow_batch.ga
A test/base/data/test_workflow_map_reduce_pause.ga
A test/base/data/test_workflow_matching_lists.ga
A test/base/data/test_workflow_missing_tool.ga
A test/base/data/test_workflow_pause.ga
A test/base/data/test_workflow_topoambigouity.ga
A test/base/data/test_workflow_topoambigouity_auto_laidout.ga
A test/base/data/test_workflow_validation_1.ga
A test/base/data/test_workflow_with_runtime_input.ga
M test/base/driver_util.py
A test/base/populators.py
A test/base/workflows_format_2/README.txt
A test/base/workflows_format_2/__init__.py
A test/base/workflows_format_2/converter.py
A test/base/workflows_format_2/interface.py
A test/base/workflows_format_2/main.py
R test/casperjs/api-dataset-tests.js
R test/casperjs/api-visualizations-tests.js
M test/docker/README.md
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/checksum.xml
M test/functional/tools/column_param.xml
A test/functional/tools/compressed_bz2_fastq_conversion.xml
A test/functional/tools/compressed_bz2_fastq_no_conversion.xml
A test/functional/tools/compressed_gz_fastq_conversion.xml
A test/functional/tools/compressed_gz_fastq_no_conversion.xml
A test/functional/tools/explicit_conversion.xml
A test/functional/tools/for_workflows/mapper2.xml
A test/functional/tools/implicit_conversion.xml
A test/functional/tools/is_valid_xml.xml
A test/functional/tools/legacy_r.xml
M test/functional/tools/md5sum.xml
A test/functional/tools/mulled_example_conflict.xml
A test/functional/tools/param_text_option.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/config/phdcomics.yaml
A test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/static/script.js
A test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/trans_object/config/trans_object.yaml
A test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/static/script.js
A test/functional/webhooks/xkcd/static/styles.css
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/galaxy_selenium/sizzle.py
A test/integration/resubmission_default_job_conf.xml
M test/integration/resubmission_runners.py
M test/integration/test_job_resubmission.py
M test/integration/test_resolvers.py
M test/manual/workflows_scaling.py
M test/qunit/tests/workflow_editor_tests.js
A test/selenium_tests/_workflow_fixtures.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
A test/selenium_tests/test_workflow_management.py
A test/selenium_tests/test_workflow_run.py
M test/unit/jobs/test_job_configuration.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tools/evolution/add_scores.xml
M tools/extract/extract_genomic_dna.xml
M tools/filters/pasteWrapper.xml
M tools/maf/genebed_maf_to_fasta.xml
M tools/maf/interval2maf.xml
M tools/maf/interval2maf_pairwise.xml
M tools/maf/interval_maf_to_merged_fasta.xml
M tools/maf/macros.xml
M tools/maf/maf_by_block_number.xml
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_limit_to_species.xml
M tools/maf/maf_reverse_complement.xml
M tools/maf/maf_split_by_species.xml
M tools/maf/maf_stats.xml
M tools/maf/maf_thread_for_species.xml
M tools/maf/maf_to_bed.xml
M tools/maf/maf_to_fasta.xml
M tools/maf/maf_to_interval.xml
M tools/maf/vcf_to_maf_customtrack.xml
M tools/metag_tools/shrimp_color_wrapper.xml
M tools/metag_tools/shrimp_wrapper.xml
M tools/next_gen_conversion/fastq_gen_conv.xml
M tools/plotting/bar_chart.xml
M tools/stats/aggregate_binned_scores_in_intervals.xml
M tox.ini
Log Message:
-----------
Merge -dev.
Commit: 03ae0d5d6f5c278e0d1d501f68aef49e4f63ff7c
https://github.com/galaxyproject/galaxy/commit/03ae0d5d6f5c278e0d1d501f68ae…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/toolshed/util.js
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/buildapp.py
A static/maps/mvc/toolshed/categories-view.js.map
A static/maps/mvc/toolshed/repositories-view.js.map
A static/maps/mvc/toolshed/repository-queue-view.js.map
A static/maps/mvc/toolshed/repository-view.js.map
A static/maps/mvc/toolshed/shed-list-view.js.map
A static/maps/mvc/toolshed/util.js.map
M static/scripts/admin.toolshed.js
A static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/util.js
Log Message:
-----------
Fix installation from queue, add repository installation status view.
Commit: 259c3c5f99522d0b4f0e62f24386ce11548fc3cc
https://github.com/galaxyproject/galaxy/commit/259c3c5f99522d0b4f0e62f24386…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-09 (Thu, 09 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/libs/jquery/jquery.autocomplete.js
M client/galaxy/scripts/mvc/form/form-input.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-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-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/ui/autocom_tagging.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.xml
M config/plugins/tours/core.history.yaml
M contrib/nagios/check_galaxy
M contrib/nagios/check_galaxy.py
R doc/source/lib/galaxy_utils.rst
R doc/source/lib/galaxy_utils.sequence.rst
M doc/source/lib/modules.rst
A doc/source/releases/17.01.rst
M doc/source/releases/17.01_announce.rst
A doc/source/releases/17.05_announce.rst
M doc/source/releases/_thanks.rst
M doc/source/releases/index.rst
M lib/galaxy/config.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0093_add_job_params_col.py
M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py
M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py
M lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py
M lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py
M lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py
M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
M lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py
M lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py
M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
M lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0121_workflow_uuids.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0132_add_lastpasswordchange_to_user.py
M lib/galaxy/model/migrate/versions/0133_add_dependency_column_to_job.py
A lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/steps.py
R lib/galaxy_utils/__init__.py
R lib/galaxy_utils/sequence/__init__.py
R lib/galaxy_utils/sequence/fasta.py
R lib/galaxy_utils/sequence/fastq.py
R lib/galaxy_utils/sequence/sequence.py
R lib/galaxy_utils/sequence/transform.py
R lib/galaxy_utils/sequence/vcf.py
M scripts/bootstrap_history.py
M static/maps/libs/jquery/jquery.autocomplete.js.map
M static/maps/mvc/form/form-input.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-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-misc.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/ui/autocom_tagging.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/libs/jquery/jquery.autocomplete.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/ui/autocom_tagging.js
M templates/webapps/tool_shed/repository/tool_form.mako
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/qunit/tests/form_tests.js
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HistoryManager.py
Log Message:
-----------
Merge with -dev.
Commit: b15fdf080ad86e157829e312da056829710dae12
https://github.com/galaxyproject/galaxy/commit/b15fdf080ad86e157829e312da05…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
A client/galaxy/scripts/mvc/toolshed/workflows-view.js
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M static/scripts/admin.toolshed.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/workflows-view.js
Log Message:
-----------
Enable preview of repository from workflows missing tools.
Commit: dbbcdee9abb88e2479574c9d410fa50cd29b2b41
https://github.com/galaxyproject/galaxy/commit/dbbcdee9abb88e2479574c9d410f…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M CONTRIBUTING.md
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M config/datatypes_conf.xml.sample
M config/plugins/tours/core.galaxy_ui.yaml
M doc/source/slideshow/architecture/galaxy_architecture.md
M doc/source/slideshow/architecture/images/hda_dataset.plantuml.svg
M doc/source/slideshow/architecture/images/hda_hdca.plantuml.svg
M doc/source/slideshow/architecture/images/objectstore.plantuml.svg
M doc/source/slideshow/architecture/images/plantuml_options.txt
M doc/source/slideshow/architecture/images/server_client.plantuml.svg
M doc/source/slideshow/architecture/images/server_client_old.plantuml.svg
M doc/source/slideshow/architecture/images/webapp.plantuml.svg
M doc/source/slideshow/architecture/style.css
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/steps.py
M scripts/slideshow/slideshow_template.html
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/user/user-quotameter.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/user/user-quotameter.js
M templates/admin/reload_tool.mako
M test/api/test_tools.py
M test/api/test_workflow_extraction.py
M test/base/populators.py
A test/functional/tools/output_format_deprecated_when.xml
M test/functional/tools/samples_tool_conf.xml
M test/selenium_tests/framework.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_uploads.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: e3eecfc0ec7994aa0385a7d3a4e38ebde0c9125e
https://github.com/galaxyproject/galaxy/commit/e3eecfc0ec7994aa0385a7d3a4e3…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-14 (Tue, 14 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
Log Message:
-----------
Fix repository queue view.
Commit: 64ad2fcf084218e9dea63dc0ade49314b650a721
https://github.com/galaxyproject/galaxy/commit/64ad2fcf084218e9dea63dc0ade4…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M lib/galaxy/webapps/galaxy/api/toolshed.py
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
Log Message:
-----------
Implement adding a workflow repository to the installation queue.
Commit: da9c57d3656a61c8da31322d54702e509bb69232
https://github.com/galaxyproject/galaxy/commit/da9c57d3656a61c8da31322d5470…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/workflow/workflow-view.js
M templates/webapps/galaxy/workflow/editor.mako
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: 9688b7ba4d08b63033ddd407b9944cf96e4f4032
https://github.com/galaxyproject/galaxy/commit/9688b7ba4d08b63033ddd407b994…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-15 (Wed, 15 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
Log Message:
-----------
Fix discovering a repository for workflows.
Commit: afc7b1c2cd0641d2b57821c5c1a8e0e245a2ad54
https://github.com/galaxyproject/galaxy/commit/afc7b1c2cd0641d2b57821c5c1a8…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
Log Message:
-----------
Fix styling for repository installation status.
Commit: 233b90c610b8ed3d8067da7a4b4944ab6d322000
https://github.com/galaxyproject/galaxy/commit/233b90c610b8ed3d8067da7a4b49…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M static/scripts/admin.toolshed.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
Log Message:
-----------
Style the repository queue properly.
Commit: 661e93a139ba5189856d8189886dcce8ac06d7d6
https://github.com/galaxyproject/galaxy/commit/661e93a139ba5189856d8189886d…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
A config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
A scripts/secret_decoder_ring.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: ba1ccce10af37ebd84b83a77ad7b764ab4d9efe5
https://github.com/galaxyproject/galaxy/commit/ba1ccce10af37ebd84b83a77ad7b…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/toolshed/workflows-view.js
Log Message:
-----------
Remove superfluous commands.
Commit: 6aa167ba50c3f4f31a7b0c637f88b1d7400dc501
https://github.com/galaxyproject/galaxy/commit/6aa167ba50c3f4f31a7b0c637f88…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repositories-view.js
Log Message:
-----------
Made search results more readable.
Commit: 73773d269ba4bb014f99d5230fd8ecdc811ede52
https://github.com/galaxyproject/galaxy/commit/73773d269ba4bb014f99d5230fd8…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-16 (Thu, 16 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Remove queue button from installed repos.
Commit: e0bb34cdf5e4ffa6927c758ba03823f1160966c3
https://github.com/galaxyproject/galaxy/commit/e0bb34cdf5e4ffa6927c758ba038…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M doc/source/releases/17.01_announce.rst
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/parameters/basic.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_execution.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: 68a51acc5395d5a2af0c5a68bf756fe41b14c9f2
https://github.com/galaxyproject/galaxy/commit/68a51acc5395d5a2af0c5a68bf75…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
Log Message:
-----------
Correct errors revealed by travis.
Commit: 5dc9728d29bc4c0c8b587dc30cd492a87193065a
https://github.com/galaxyproject/galaxy/commit/5dc9728d29bc4c0c8b587dc30cd4…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Mostly fixed repository dependency jstree.
Commit: fdf95d3702118cfee16dd904dc461898316b7bf9
https://github.com/galaxyproject/galaxy/commit/fdf95d3702118cfee16dd904dc46…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-02-21 (Tue, 21 Feb 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form-workflow.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/galaxy.ini.sample
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run_request.py
M lib/tool_shed/util/workflow_util.py
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form-workflow.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form-workflow.js
M static/scripts/mvc/workflow/workflow-view.js
Log Message:
-----------
Merge dev.
Commit: fbe557f09b86c97700043a5bd4222b62d9d0d49a
https://github.com/galaxyproject/galaxy/commit/fbe557f09b86c97700043a5bd422…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M .ci/flake8_blacklist.txt
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
R client/galaxy/scripts/mvc/tool/tool-form-workflow.js
A client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/phinch/config/phinch.ini.sample
M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A cron/clean_docker_swarm_mode_services.sh
M doc/source/admin/interactive_environments.rst
M doc/source/releases/17.01_announce.rst
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/proteomics.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/dynamic_tool_destination.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/search/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/modules.py
M scripts/bootstrap_history.py
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/form/form-section.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form-workflow.js.map
A static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form-workflow.js
A static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-view.js
M templates/grid_base.mako
A templates/webapps/galaxy/user/manage_info.mako
M test/api/test_workflows.py
A test/functional/tools/mulled_example_multi_incomplete.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/workflows/test_modules.py
M tools/data_source/upload.py
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: fb5005bba40d1d1b53b826ab620686662d42c39e
https://github.com/galaxyproject/galaxy/commit/fb5005bba40d1d1b53b826ab6206…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-03-06 (Mon, 06 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M lib/galaxy/tools/__init__.py
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/webhooks.js
Log Message:
-----------
Fix incorrect merge.
Commit: 9309cecef039e6a00eb944c6b6d445e8e935c1cf
https://github.com/galaxyproject/galaxy/commit/9309cecef039e6a00eb944c6b6d4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
Log Message:
-----------
add small stylystic changes
Commit: 0ba78254e57b8f0fd2c8c64a36c4385f3a8bda87
https://github.com/galaxyproject/galaxy/commit/0ba78254e57b8f0fd2c8c64a36c4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M static/maps/admin.toolshed.js.map
M static/maps/mvc/toolshed/categories-view.js.map
A static/maps/mvc/toolshed/repo-status-view.js.map
M static/maps/mvc/toolshed/repositories-view.js.map
M static/maps/mvc/toolshed/repository-queue-view.js.map
M static/maps/mvc/toolshed/repository-view.js.map
M static/maps/mvc/toolshed/shed-list-view.js.map
M static/maps/mvc/toolshed/toolshed-model.js.map
M static/maps/mvc/toolshed/util.js.map
A static/maps/mvc/toolshed/workflows-view.js.map
M static/scripts/admin.toolshed.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/ui/ui-thumbnails.js
Log Message:
-----------
repack client (seems to not be done in a while)
Commit: 6ba72513e492609e81095cd6c7a75c9c4eb908c6
https://github.com/galaxyproject/galaxy/commit/6ba72513e492609e81095cd6c7a7…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M .ci/py3_sources.txt
M README.rst
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/layout/menu.js
A client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui.less
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
A config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/static/script.js
A config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/tool_list/config/tool_list.yml
A config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/swarm_manager_conf.yml.sample
R cron/clean_docker_swarm_mode_services.sh
A doc/source/admin/authentication.md
R doc/source/admin/chat-0.png
R doc/source/admin/chat-1.png
R doc/source/admin/chat-2.png
R doc/source/admin/chat-3.png
R doc/source/admin/chat-4.png
R doc/source/admin/chat.rst
R doc/source/admin/communication_server.png
R doc/source/admin/communication_server_rooms.png
M doc/source/admin/dependency_resolvers.rst
R doc/source/admin/grt.rst
R doc/source/admin/images_webhooks/history-menu.png
R doc/source/admin/images_webhooks/masthead.png
R doc/source/admin/images_webhooks/masthead_trans_object.png
R doc/source/admin/images_webhooks/tool.png
R doc/source/admin/images_webhooks/workflow.png
M doc/source/admin/index.rst
R doc/source/admin/interactive_environments.png
R doc/source/admin/interactive_environments.rst
R doc/source/admin/interactive_environments.svg
R doc/source/admin/mulled_containers.rst
A doc/source/admin/special_topics/chat-0.png
A doc/source/admin/special_topics/chat-1.png
A doc/source/admin/special_topics/chat-2.png
A doc/source/admin/special_topics/chat-3.png
A doc/source/admin/special_topics/chat-4.png
A doc/source/admin/special_topics/chat.rst
A doc/source/admin/special_topics/communication_server.png
A doc/source/admin/special_topics/communication_server_rooms.png
A doc/source/admin/special_topics/grt.rst
A doc/source/admin/special_topics/images_webhooks/history-menu.png
A doc/source/admin/special_topics/images_webhooks/masthead.png
A doc/source/admin/special_topics/images_webhooks/masthead_trans_object.png
A doc/source/admin/special_topics/images_webhooks/tool.png
A doc/source/admin/special_topics/images_webhooks/workflow.png
A doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/interactive_environments.png
A doc/source/admin/special_topics/interactive_environments.rst
A doc/source/admin/special_topics/interactive_environments.svg
A doc/source/admin/special_topics/mulled_containers.rst
A doc/source/admin/special_topics/webhooks.rst
A doc/source/admin/tool_panel.rst
R doc/source/admin/webhooks.rst
M doc/source/conf.py
M doc/source/dev/index.rst
M doc/source/dev/interactive_environments.rst
M doc/source/index.rst
M doc/source/project/issues.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
A lib/galaxy/container/__init__.py
A lib/galaxy/container/docker_swarm.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
R lib/galaxy/tags/__init__.py
R lib/galaxy/tags/tag_handler.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__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/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
A lib/galaxy/tools/fetcher.py
M lib/galaxy/tools/loader_directory.py
A lib/galaxy/tools/locations/__init__.py
A lib/galaxy/tools/locations/dockstore.py
A lib/galaxy/tools/locations/file.py
A lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/json.py
R lib/galaxy/util/postfork.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M 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/mapper.js
A lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
A lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/util.py
M lib/galaxy/workflow/steps.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M run_tests.sh
M scripts/api/README
M scripts/secret_decoder_ring.py
A static/maps/analysis.js.map
A static/maps/app.js.map
A static/maps/app/analysis.js.map
M static/maps/galaxy.interactive_environments.js.map
M static/maps/layout/menu.js.map
A static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li-edit.js.map
M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/user/user-preferences.js.map
A static/scripts/analysis.js
A static/scripts/app.js
A static/scripts/app/analysis.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/layout/menu.js
A static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/user/user-preferences.js
M static/style/blue/base.css
M templates/grid_base.mako
M templates/webapps/galaxy/admin/index.mako
A templates/webapps/galaxy/admin/manage_dependencies.mako
R templates/webapps/galaxy/user/manage_info.mako
M templates/webapps/tool_shed/repository/common.mako
M test/TESTING.md
M test/docker/base/run_test_wrapper.sh
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
M test/integration/test_resolvers.py
A test/selenium_tests/test_collection_builders.py
M test/unit/tools/test_data_parameters.py
Log Message:
-----------
Merge with -dev.
Commit: 0d87bb58805cb1ec1ee45f5c9c6557e56154a2cf
https://github.com/galaxyproject/galaxy/commit/0d87bb58805cb1ec1ee45f5c9c65…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-03-21 (Tue, 21 Mar 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Remove duplicate import.
Commit: a1f110be7eb86ccf2d72a4bb93c2b61999c9aeae
https://github.com/galaxyproject/galaxy/commit/a1f110be7eb86ccf2d72a4bb93c2…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-12 (Wed, 12 Apr 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
M CONTRIBUTING.md
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tag.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-table.js
A client/galaxy/scripts/mvc/upload/collection/collection-row.js
A client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/upload-view.js
A client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-preferences.js
A client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/ui/paired-collection-creator.less
M client/galaxy/style/less/upload.less
M client/package.json
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/ethercalc/config/allowed_images.yml.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.ini.sample
A config/plugins/interactive_environments/ethercalc/config/ethercalc.xml
A config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
A config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_basic.js.map
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
A config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
A config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
M config/plugins/visualizations/charts/static/repository/registry.json
A config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
M config/plugins/visualizations/charts/static/repository/utilities/utils.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/basic/wrapper.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
A config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
M config/tool_destinations.yml.sample
M display_applications/igv/bigwig.xml
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/index.rst
A doc/source/admin/reports.md
M doc/source/admin/useful_scripts.rst
A doc/source/api/api.rst
A doc/source/api/ts_api.rst
M doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/galaxy.webapps.galaxy.api.rst
R doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/releases/_header.rst
M doc/source/ts_api_doc.rst
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/unzip_collection.xml
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/zip_collection.xml
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
R lib/galaxy/webapps/galaxy/controllers/search.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M run_tests.sh
A static/GruntFile.js
A static/GruntFile.js.map
M static/maps/layout/menu.js.map
M static/maps/mvc/collection/base-creator.js.map
M static/maps/mvc/collection/collection-view-edit.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/collection/list-collection-creator.js.map
M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
M static/maps/mvc/collection/pair-collection-creator.js.map
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-parameters.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-table.js.map
A static/maps/mvc/upload/collection/collection-row.js.map
A static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/upload-view.js.map
A static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-preferences.js.map
A static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.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/collection/base-creator.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-table.js
A static/scripts/mvc/upload/collection/collection-row.js
A static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/upload-view.js
A static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
A static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/style/blue/base.css
R templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
M templates/admin/tool_shed_repository/select_tool_panel_section.mako
R templates/user/dbkeys.mako
M templates/webapps/galaxy/admin/manage_dependencies.mako
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api_asserts.py
M test/base/data/test_workflow_pause.ga
M test/base/driver_util.py
M test/base/populators.py
M test/functional/tools/create_10.xml
A test/functional/tools/create_2.xml
A test/functional/tools/identifier_multiple_in_conditional.xml
A test/functional/tools/identifier_multiple_in_repeat.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_job_conf.xml
M test/qunit/package.json
M test/qunit/test-data/paired-collection-creator.data.js
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M tool-data/shared/ucsc/builds.txt.sample
M tool-data/shared/ucsc/ucsc_build_sites.txt.sample
M tools/filters/trimmer.py
M tools/filters/trimmer.xml
Log Message:
-----------
Merge with dev.
Commit: ee755cb47ad6f8401f02e452e940941b71ce1fe8
https://github.com/galaxyproject/galaxy/commit/ee755cb47ad6f8401f02e452e940…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M .ci/flake8_docstrings_include_list.txt
M .ci/flake8_lint_include_list.txt
M .ci/py3_sources.txt
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/style/less/ui.less
A config/containers_conf.yml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/tool_conf.xml.sample
M lib/galaxy/config.py
R lib/galaxy/container/__init__.py
R lib/galaxy/container/docker_swarm.py
A lib/galaxy/containers/__init__.py
A lib/galaxy/containers/docker.py
A lib/galaxy/containers/docker_decorators.py
A lib/galaxy/containers/docker_model.py
A lib/galaxy/containers/docker_swarm.py
A lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/evaluation.py
A lib/galaxy/tools/filter_from_file.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/wrapped.py
A lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/wrappers.py
A lib/galaxy/util/handlers.py
M lib/galaxy/util/submodules.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/workflow/scheduling_manager.py
M static/maps/galaxy.interactive_environments.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/style/blue/base.css
M templates/show_params.mako
M templates/webapps/galaxy/workflow/display.mako
A test-data/filter_labels_1.txt
A test-data/new_labels_1.txt
A test-data/new_labels_2.txt
A test-data/new_labels_bad_1.txt
A test-data/new_labels_bad_2.txt
M test/functional/tools/samples_tool_conf.xml
M test/integration/test_workflow_handler_configuration.py
A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Merge in dev.
Commit: 88a3ee1073b939bb161980389f5d55abc483439f
https://github.com/galaxyproject/galaxy/commit/88a3ee1073b939bb161980389f5d…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M config/openid_conf.xml.sample
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/managers/citations.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py
M lib/galaxy/model/migrate/versions/0119_job_metrics.py
M lib/galaxy/model/migrate/versions/0120_dataset_collections.py
M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py
M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py
M lib/galaxy/model/migrate/versions/0124_job_state_history.py
M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py
M lib/galaxy/model/migrate/versions/0126_password_reset.py
M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py
M lib/galaxy/model/migrate/versions/0128_session_timeout.py
M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py
M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py
M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/verify/asserts/__init__.py
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/visualization/genomes.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/tool_migration_manager.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/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
R openid/google.xml
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: 1d620ef260297affe8947fa57d5f542ce418e769
https://github.com/galaxyproject/galaxy/commit/1d620ef260297affe8947fa57d5f…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-04-24 (Mon, 24 Apr 2017)
Changed paths:
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M static/maps/layout/menu.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/locale.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/nls/fr/locale.js
M static/scripts/nls/locale.js
Log Message:
-----------
Merge branch 'dev' of git://github.com/galaxyproject/galaxy into ts_api_backbone
Commit: 272fbd2235aeaa9ea9d9b257958c8a14301d8e7b
https://github.com/galaxyproject/galaxy/commit/272fbd2235aeaa9ea9d9b257958c…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/config.py
Log Message:
-----------
enable TS beta isntallation interface by default
Commit: b9fb2de42b53fcb1516422cdd3d40177d507529a
https://github.com/galaxyproject/galaxy/commit/b9fb2de42b53fcb1516422cdd3d4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/mvc/toolshed/categories-view.js
A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repo-status-view.js
A client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repository-view.js
A client/galaxy/scripts/mvc/toolshed/shed-list-view.js
A client/galaxy/scripts/mvc/toolshed/toolshed-model.js
A client/galaxy/scripts/mvc/toolshed/util.js
A client/galaxy/scripts/mvc/toolshed/workflows-view.js
M config/galaxy.ini.sample
M lib/galaxy/config.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
A lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/tool_shed/util/repository_util.py
A static/maps/admin.toolshed.js.map
A static/maps/mvc/toolshed/categories-view.js.map
A static/maps/mvc/toolshed/repo-queue-view.js.map
A static/maps/mvc/toolshed/repo-status-view.js.map
A static/maps/mvc/toolshed/repositories-view.js.map
A static/maps/mvc/toolshed/repository-queue-view.js.map
A static/maps/mvc/toolshed/repository-view.js.map
A static/maps/mvc/toolshed/shed-category-view.js.map
A static/maps/mvc/toolshed/shed-list-view.js.map
A static/maps/mvc/toolshed/shed-repo-details-view.js.map
A static/maps/mvc/toolshed/shed-repo-list-view.js.map
A static/maps/mvc/toolshed/sheds-list-view.js.map
A static/maps/mvc/toolshed/toolshed-model.js.map
A static/maps/mvc/toolshed/util.js.map
A static/maps/mvc/toolshed/workflows-view.js.map
A static/scripts/admin.toolshed.js
A static/scripts/mvc/toolshed/categories-view.js
A static/scripts/mvc/toolshed/repo-queue-view.js
A static/scripts/mvc/toolshed/repo-status-view.js
A static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-queue-view.js
A static/scripts/mvc/toolshed/repository-view.js
A static/scripts/mvc/toolshed/shed-category-view.js
A static/scripts/mvc/toolshed/shed-list-view.js
A static/scripts/mvc/toolshed/shed-repo-details-view.js
A static/scripts/mvc/toolshed/shed-repo-list-view.js
A static/scripts/mvc/toolshed/sheds-list-view.js
A static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/util.js
A static/scripts/mvc/toolshed/workflows-view.js
R templates/admin/tool_shed_repository/browse_toolsheds.mako
Log Message:
-----------
Merge pull request #3626 from davebx/ts_api_backbone
API installation of toolshed repositories.
Compare: https://github.com/galaxyproject/galaxy/compare/5eadd4842dcd...b9fb2de42b53