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November 2017
- 1 participants
- 160 discussions
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: f1d2455635aec3d88c354061f106adb53081465f
https://github.com/galaxyproject/usegalaxy-playbook/commit/f1d2455635aec3d8…
Author: Dave B <dave(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M env/test/files/galaxy/var/integrated_tool_panel.xml
M env/test/files/galaxy/var/shed_tool_conf.xml
M env/test/files/galaxy/var/shed_tool_data_table_conf.xml
Log Message:
-----------
Installed MiModD 0.8.1
1
0
[galaxyproject/usegalaxy-playbook] f01373: Fix BAM metadata issues on Jetstream
by GitHub 15 Nov '17
by GitHub 15 Nov '17
15 Nov '17
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: f01373fe9596a3eafec883d7c3bcc76cab433c91
https://github.com/galaxyproject/usegalaxy-playbook/commit/f01373fe9596a3ea…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M CHANGELOG.md
M env/main/templates/galaxy/config/job_conf.xml.j2
M env/test/templates/galaxy/config/job_conf.xml.j2
Log Message:
-----------
Fix BAM metadata issues on Jetstream
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f
https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Add missing ipaddress requirement
Broken in https://github.com/galaxyproject/galaxy/pull/4289 .
Fix https://github.com/galaxyproject/galaxy/issues/4999 .
Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623
https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement
[17.09] Add missing ipaddress requirement
Commit: 7bede53beff349b393c3c5a293902def1d8bdb76
https://github.com/galaxyproject/galaxy/commit/7bede53beff349b393c3c5a29390…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Merge branch 'release_17.09' into dev
Conflicts:
lib/galaxy/dependencies/pinned-requirements.txt
lib/galaxy/dependencies/requirements.txt
Compare: https://github.com/galaxyproject/galaxy/compare/f34e6a1e2e18...7bede53beff3
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c994005fcc2b06bacfaf992be9de9002c47b5ab3
https://github.com/galaxyproject/galaxy/commit/c994005fcc2b06bacfaf992be9de…
Author: xgaia <xgaia(a)gmx.com>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
A config/plugins/interactive_environments/askomics/LICENSE
A config/plugins/interactive_environments/askomics/README.md
A config/plugins/interactive_environments/askomics/config/allowed_images.yml
A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample
A config/plugins/interactive_environments/askomics/config/askomics.ini.sample
A config/plugins/interactive_environments/askomics/config/askomics.xml
A config/plugins/interactive_environments/askomics/static/js/askomics.js
A config/plugins/interactive_environments/askomics/templates/askomics.mako
Log Message:
-----------
add askomics interactive environment
Commit: 4d5facb9857e2f7b70282e74f40d0b31d1120d41
https://github.com/galaxyproject/galaxy/commit/4d5facb9857e2f7b70282e74f40d…
Author: xgaia <xgaia(a)gmx.com>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
R config/plugins/interactive_environments/askomics/README.md
R config/plugins/interactive_environments/askomics/config/allowed_images.yml
Log Message:
-----------
remove files
Commit: e55121f655ca105f2d9ac7ea473cca77c6f07b75
https://github.com/galaxyproject/galaxy/commit/e55121f655ca105f2d9ac7ea473c…
Author: xgaia <xgaia(a)gmx.com>
Date: 2017-10-03 (Tue, 03 Oct 2017)
Changed paths:
R config/plugins/interactive_environments/askomics/LICENSE
Log Message:
-----------
remove license file
Commit: 04370ebff931ed2f591531f2cf58b8248e71f956
https://github.com/galaxyproject/galaxy/commit/04370ebff931ed2f591531f2cf58…
Author: xgaia <xgaia(a)gmx.com>
Date: 2017-10-05 (Thu, 05 Oct 2017)
Changed paths:
M config/plugins/interactive_environments/askomics/templates/askomics.mako
Log Message:
-----------
use build-in password generator for api key
Commit: 1d5f0d2b611c3685cc12b95a0efdb91e3e4d872b
https://github.com/galaxyproject/galaxy/commit/1d5f0d2b611c3685cc12b95a0efd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M config/plugins/interactive_environments/askomics/static/js/askomics.js
M config/plugins/interactive_environments/askomics/templates/askomics.mako
Log Message:
-----------
Fixes to askomics javascript
Commit: 7d674e1de0d23b48d3f6a8cf0fc4c5a2d883d9e7
https://github.com/galaxyproject/galaxy/commit/7d674e1de0d23b48d3f6a8cf0fc4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M config/plugins/interactive_environments/askomics/static/js/askomics.js
Log Message:
-----------
Left off semicolon.
Commit: 8d3c8c6d40521ec513b936dd4b15693edf0f280b
https://github.com/galaxyproject/galaxy/commit/8d3c8c6d40521ec513b936dd4b15…
Author: Xavier Garnier <xgaia(a)gmx.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M config/plugins/interactive_environments/askomics/static/js/askomics.js
M config/plugins/interactive_environments/askomics/templates/askomics.mako
Log Message:
-----------
Merge pull request #1 from dannon/askomics-fixes
Small javascript fixes for askomics IE integration
Commit: f34e6a1e2e182c10a36172d63740559723058086
https://github.com/galaxyproject/galaxy/commit/f34e6a1e2e182c10a36172d63740…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample
A config/plugins/interactive_environments/askomics/config/askomics.ini.sample
A config/plugins/interactive_environments/askomics/config/askomics.xml
A config/plugins/interactive_environments/askomics/static/js/askomics.js
A config/plugins/interactive_environments/askomics/templates/askomics.mako
Log Message:
-----------
Merge pull request #4737 from xgaia/askomics-ie
AskOmics Interactive Environment
Compare: https://github.com/galaxyproject/galaxy/compare/e27a16953d5f...f34e6a1e2e18
1
0
[galaxyproject/galaxy] 140a0a: Add DELETE /api/jobs/<job_id> as a job cancellatio...
by GitHub 15 Nov '17
by GitHub 15 Nov '17
15 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 140a0a49d3af5f5d6ffaa50cc0cac5b5f4cd1bcc
https://github.com/galaxyproject/galaxy/commit/140a0a49d3af5f5d6ffaa50cc0ca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-08 (Wed, 08 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
M test/base/populators.py
A test/functional/tools/cat_data_and_sleep.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
A test/integration/test_local_job_cancellation.py
Log Message:
-----------
Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint.
Commit: e27a16953d5faadbfa8d2be1e0a09afe4bd7df87
https://github.com/galaxyproject/galaxy/commit/e27a16953d5faadbfa8d2be1e0a0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/jobs.py
M test/base/populators.py
A test/functional/tools/cat_data_and_sleep.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/navigates_galaxy.py
A test/integration/test_local_job_cancellation.py
Log Message:
-----------
Merge pull request #4961 from jmchilton/job_delete_api
Add DELETE /api/jobs/<job_id> as a job cancellation API endpoint.
Compare: https://github.com/galaxyproject/galaxy/compare/bbd96c435b86...e27a16953d5f
1
0
[galaxyproject/galaxy] a1e912: If installing dev dependencies, do so along side r...
by GitHub 15 Nov '17
by GitHub 15 Nov '17
15 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a1e91231aa5dba34c10f039446177d0f55871623
https://github.com/galaxyproject/galaxy/commit/a1e91231aa5dba34c10f03944617…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-02 (Thu, 02 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M scripts/common_startup.sh
Log Message:
-----------
If installing dev dependencies, do so along side regular dependencies.
Catch conflicts and works faster.
Commit: bbd96c435b866a2cab7299fadf0687d7e2c99e3e
https://github.com/galaxyproject/galaxy/commit/bbd96c435b866a2cab7299fadf06…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #4903 from jmchilton/dev_at_same_time
Install dev and regular dependencies at the same time.
Compare: https://github.com/galaxyproject/galaxy/compare/54c6a794e9c6...bbd96c435b86
1
0
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f
https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Add missing ipaddress requirement
Broken in https://github.com/galaxyproject/galaxy/pull/4289 .
Fix https://github.com/galaxyproject/galaxy/issues/4999 .
Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623
https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement
[17.09] Add missing ipaddress requirement
Compare: https://github.com/galaxyproject/galaxy/compare/b25de8b00316...18467e9b2cec
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6c32edebc1b36136759a055fe3032d51a24f1f68
https://github.com/galaxyproject/galaxy/commit/6c32edebc1b36136759a055fe303…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-10-17 (Tue, 17 Oct 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
A test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
start writing tests for TDT
Commit: 7431cb13123f091fc13d5cb2b2756a4bd0726d1f
https://github.com/galaxyproject/galaxy/commit/7431cb13123f091fc13d5cb2b275…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-10-17 (Tue, 17 Oct 2017)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/static/script.js
Log Message:
-----------
fix TDT's dependency
Commit: b0973391640248f29765bacdc0ff0faf68db5f52
https://github.com/galaxyproject/galaxy/commit/b0973391640248f29765bacdc0ff…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-10-17 (Tue, 17 Oct 2017)
Changed paths:
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
test successful tour generation
Commit: 9d646c605cbab0c59e34379818e2e63f7269e5b6
https://github.com/galaxyproject/galaxy/commit/9d646c605cbab0c59e34379818e2…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-11-01 (Wed, 01 Nov 2017)
Changed paths:
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
improve the test
Commit: 323e1ad64e9f3fa75c32a283b82694474d49ceb0
https://github.com/galaxyproject/galaxy/commit/323e1ad64e9f3fa75c32a283b826…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-11-01 (Wed, 01 Nov 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
R .ci/flake8_py3_wrapper.sh
M .ci/jenkins/selenium/Dockerfile
M .ci/jenkins/selenium/docker-compose.yml
M .ci/jenkins/selenium/galaxy.ini
M .ci/jenkins/selenium/run_galaxy.bash
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
A .ci/tox_envs/flake8/Pipfile
A .ci/tox_envs/flake8/requirements.txt
A .ci/tox_envs/flake8_imports/Pipfile
A .ci/tox_envs/flake8_imports/requirements.txt
A .ci/tox_envs/update.sh
M .gitignore
M .travis.yml
M CITATION
M Makefile
A client/.babelrc
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/i18n.js
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/backbone.js
R client/galaxy/scripts/libs/bibtex.js
R client/galaxy/scripts/libs/d3.js
R client/galaxy/scripts/libs/jquery.complexify.js
R client/galaxy/scripts/libs/jquery/jquery.cookie.js
R client/galaxy/scripts/libs/jquery/jquery.js
R client/galaxy/scripts/libs/jquery/jquery.migrate.js
R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js
R client/galaxy/scripts/libs/raven.js
R client/galaxy/scripts/libs/require.js
R client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.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/data.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/dataset/states.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-preferences.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-dag.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/job/job-params.js
A client/galaxy/scripts/mvc/lazy/lazy-limited.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-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/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
A client/galaxy/scripts/mvc/library/library-util.js
M client/galaxy/scripts/mvc/list/list-item.js
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M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/job/job-params.js
A static/scripts/mvc/lazy/lazy-limited.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
A static/scripts/mvc/library/library-util.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tag.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.js
M static/scripts/mvc/tool/tool-genomespace.js
R static/scripts/mvc/tool/tool-template.js
R static/scripts/mvc/tool/tool-webhooks.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-queue-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
R static/scripts/mvc/toolshed/shed-category-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
R static/scripts/mvc/toolshed/shed-repo-details-view.js
R static/scripts/mvc/toolshed/shed-repo-list-view.js
R static/scripts/mvc/toolshed/sheds-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/tours.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/icon-button.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-select-ftp.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/collection/collection-row.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
A static/scripts/mvc/upload/upload-extension.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/change-password.js
R static/scripts/mvc/user/extra-information.js
R static/scripts/mvc/user/manage-user-information.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/de/locale.js
M static/scripts/nls/es/locale.js
M 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/scripts/onload.js
R static/scripts/packed
M static/scripts/polyfills.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/ui/editable-text.js
M static/scripts/ui/fa-icon-button.js
M static/scripts/ui/filter-control.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/ui/popupmenu.js
M static/scripts/ui/scroll-panel.js
M static/scripts/ui/search-input.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/async-save-text.js
M static/scripts/utils/config.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/levenshtein.js
M static/scripts/utils/localization.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/natural-sort.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
M static/style/blue/base.css
M static/style/blue/library.css
R templates/admin/external_service/common.mako
R templates/admin/external_service/create_external_service.mako
R templates/admin/external_service/edit_external_service.mako
R templates/admin/external_service/grid.mako
R templates/admin/external_service/reload_external_service_types.mako
R templates/admin/external_service/view_external_service.mako
R templates/admin/forms/create_form.mako
R templates/admin/forms/edit_form_definition.mako
R templates/admin/forms/grid.mako
R templates/admin/forms/view_form_definition.mako
R templates/admin/request_type/common.mako
R templates/admin/request_type/create_request_type.mako
R templates/admin/request_type/edit_request_type.mako
R templates/admin/request_type/grid.mako
R templates/admin/request_type/request_type_permissions.mako
R templates/admin/request_type/view_request_type.mako
R templates/admin/requests/grid.mako
R templates/admin/requests/reject.mako
R templates/admin/requests/rename_datasets.mako
R templates/admin/requests/sample_datasets_grid.mako
R templates/admin/requests/view_sample_dataset.mako
R templates/admin/tool_shed_repository/browse_category.mako
R templates/admin/tool_shed_repository/initiate_repository_installation.mako
A templates/admin/tool_shed_repository/monitor_repository_installation.mako
R templates/admin/tool_shed_repository/repair_repository.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
R templates/admin/tool_shed_repository/repository_installation_grid.mako
R templates/admin/tool_shed_repository/tool_dependencies_grid.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
R templates/export_base.mako
M templates/js-app.mako
R templates/rss.mako
M templates/sharing_base.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/admin/toolsheds.mako
M templates/webapps/galaxy/galaxy.panels.mako
R templates/webapps/galaxy/history/permissions.mako
R templates/webapps/galaxy/history/rename.mako
R templates/webapps/galaxy/page/create.mako
R templates/webapps/galaxy/requests/common/add_samples.mako
R templates/webapps/galaxy/requests/common/common.mako
R templates/webapps/galaxy/requests/common/create_request.mako
R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako
R templates/webapps/galaxy/requests/common/edit_samples.mako
R templates/webapps/galaxy/requests/common/find_samples.mako
R templates/webapps/galaxy/requests/common/index.mako
R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako
R templates/webapps/galaxy/requests/common/sample_datasets.mako
R templates/webapps/galaxy/requests/common/sample_state.mako
R templates/webapps/galaxy/requests/common/view_request.mako
R templates/webapps/galaxy/requests/common/view_request_history.mako
R templates/webapps/galaxy/requests/common/view_sample.mako
R templates/webapps/galaxy/requests/common/view_sample_datasets.mako
R templates/webapps/galaxy/requests/common/view_sample_history.mako
R templates/webapps/galaxy/requests/find_samples_index.mako
R templates/webapps/galaxy/requests/grid.mako
R templates/webapps/galaxy/requests/index.mako
R templates/webapps/galaxy/visualization/create.mako
A test-data/selenium-test-notebook.ipynb
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_pages.py
M test/api/test_tools.py
A test/api/test_tools_upload.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/api_util.py
A test/base/constants.py
M test/base/populators.py
M test/base/testcase.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/collection_split_on_column.xml
A test/functional/tools/data_source.py
A test/functional/tools/empty_datasets.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/test_data_source.xml
M test/functional/twilltestcase.py
M test/functional/webhooks/phdcomics/helper/__init__.py
A test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
A test/galaxy_selenium/navigation.yml
A test/galaxy_selenium/smart_components.py
M test/integration/test_upload_configuration_options.py
M test/manual/workflows_scaling.py
M test/qunit/Gruntfile.js
M test/qunit/package.json
M test/qunit/test-app.js
M test/qunit/test-common.js
R test/qunit/test-libs/qunit-1.23.1.css
R test/qunit/test-libs/qunit-1.23.1.js
R test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-qunit-1.0.0.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/graph.js
M test/qunit/tests/hda-base.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/job-dag.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/masthead_tests.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/modal_tests.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/popover_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/utils_test.js
M test/qunit/tests/workflow_editor_tests.js
M test/selenium_tests/framework.py
M test/selenium_tests/test_anon_history.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_custom_builds.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_options.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
A test/selenium_tests/test_jupyter.py
A test/selenium_tests/test_library_contents.py
A test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_login.py
A test/selenium_tests/test_navigates_galaxy.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_registration.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
A test/unit/__init__.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
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_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.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_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_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
R test/unit/web/base/__init__.py
R test/unit/web/base/test_HookPluginManager.py
R test/unit/web/base/test_PageServingPluginManager.py
R test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.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/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/extract/liftOver_wrapper.xml
M tools/filters/axt_to_lav.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_feature_count.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_exon_bed.xml
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/genomespace/genomespace_importer.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_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/blat_wrapper.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/plotting/bar_chart.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/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tox.ini
Log Message:
-----------
Merge branch 'dev' into tdt_tests
# Conflicts:
# client/galaxy/scripts/mvc/tool/tool-form-base.js
# static/maps/mvc/tool/tool-form-base.js.map
# static/scripts/bundled/analysis.bundled.js
# static/scripts/bundled/analysis.bundled.js.map
# static/scripts/bundled/libs.bundled.js.map
# static/scripts/mvc/tool/tool-form-base.js
Commit: f419c85955dc9885ef09f77db7e10e5145ef99fd
https://github.com/galaxyproject/galaxy/commit/f419c85955dc9885ef09f77db7e1…
Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com>
Date: 2017-11-01 (Wed, 01 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M static/maps/mvc/tool/tool-form-base.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form-base.js
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
add test for TDT
Commit: c52ebfca26710b8c9883bbfdba04187d53295427
https://github.com/galaxyproject/galaxy/commit/c52ebfca26710b8c9883bbfdba04…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
A test/functional/webhooks/tour_generator
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/selenium_tests/test_tool_describing_tours.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Improvements for tour generator Selenium tests.
- Replace test using Cut1 with two tests each using framework test tools loaded with Selenium tests by default.
- Create a symbolic link so that tour generator is configured with default test webhooks.
- Establish and use components and navigates_galaxy.py abstractions for tour generation and navigation.
- In one of the tool tests actually walk the tour (previously we only verified the initial tour popover).
Commit: cecef90915abf0383aed8b56deb4ec237ca9a712
https://github.com/galaxyproject/galaxy/commit/cecef90915abf0383aed8b56deb4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
R .ci/flake8_lint_include_list.txt
R .ci/flake8_wrapper_imports.sh
A .ci/jenkins/selenium-compose/Dockerfile
A .ci/jenkins/selenium-compose/docker-compose.yml
A .ci/jenkins/selenium-compose/galaxy.ini
A .ci/jenkins/selenium-compose/run_galaxy.bash
A .ci/jenkins/selenium-compose/run_tests.sh
R .ci/jenkins/selenium/Dockerfile
R .ci/jenkins/selenium/docker-compose.yml
R .ci/jenkins/selenium/galaxy.ini
R .ci/jenkins/selenium/run_galaxy.bash
M .ci/jenkins/selenium/run_tests.sh
R .ci/tox_envs/flake8/Pipfile
R .ci/tox_envs/flake8/requirements.txt
R .ci/tox_envs/flake8_imports/Pipfile
R .ci/tox_envs/flake8_imports/requirements.txt
R .ci/tox_envs/update.sh
M .travis.yml
M Makefile
M README.rst
M client/.babelrc
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/i18n.js
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.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/data.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/dataset/states.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
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A client/galaxy/scripts/mvc/history/history-item-li.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-preferences.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
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M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/scripts/mvc/lazy/lazy-limited.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
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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/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
M client/galaxy/scripts/mvc/library/library-util.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tag.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/tool-genomespace.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
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M client/galaxy/scripts/mvc/toolshed/shed-list-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 client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/icon-button.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.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/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-extension.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
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M client/galaxy/scripts/nls/es/locale.js
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M client/galaxy/scripts/onload.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/ui/editable-text.js
M client/galaxy/scripts/ui/fa-icon-button.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/ui/popupmenu.js
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M client/galaxy/scripts/ui/search-input.js
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M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/levenshtein.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/natural-sort.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
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M client/galaxy/scripts/viz/trackster/filters.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/slotting.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/trackster/util.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/scripts/viz/viz_views.js
M client/galaxy/style/less/trackster.less
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M config/datatypes_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
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M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
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M config/plugins/interactive_environments/neo/static/js/neo.js
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M config/plugins/interactive_environments/phinch/static/js/phinch.js
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M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
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M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
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M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
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M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
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M lib/galaxy/jobs/runners/chronos.py
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M lib/galaxy/managers/datasets.py
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M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
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M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/groups.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/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/utility_containers/__init__.py
M run_tests.sh
M scripts/functional_tests.py
M scripts/manage_tool_dependencies.py
M static/maps/admin.toolshed.js.map
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M static/maps/utils/natural-sort.js.map
M static/maps/utils/query-string-parsing.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/utils/utils.js.map
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M static/scripts/layout/generic-nav-view.js
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M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
M static/style/blue/trackster.css
R templates/admin/library/grid.mako
R templates/admin/library/new_library.mako
R templates/admin/package_tool.mako
R templates/admin/reload_tool.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/show_params.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/dataset/display.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/citations.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/history/embed.mako
M templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
R templates/webapps/galaxy/library/common/browse_library.mako
R templates/webapps/galaxy/library/common/browse_library_opt.mako
R templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/library/common/folder_info.mako
R templates/webapps/galaxy/library/common/folder_permissions.mako
R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
R templates/webapps/galaxy/library/common/ldda_edit_info.mako
R templates/webapps/galaxy/library/common/ldda_info.mako
R templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_info.mako
R templates/webapps/galaxy/library/common/library_dataset_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_search_results.mako
R templates/webapps/galaxy/library/common/library_info.mako
R templates/webapps/galaxy/library/common/library_item_info.mako
R templates/webapps/galaxy/library/common/library_permissions.mako
R templates/webapps/galaxy/library/common/move_library_item.mako
R templates/webapps/galaxy/library/common/new_folder.mako
R templates/webapps/galaxy/library/common/upload.mako
R templates/webapps/galaxy/library/grid.mako
R templates/webapps/galaxy/library/index.mako
M templates/webapps/galaxy/page/editor.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/phyloviz.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/tool_shed/group/index.mako
M test/api/test_dataset_collections.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_page_revisions.py
M test/api/test_tools_upload.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/populators.py
M test/base/testcase.py
M test/docker/base/Dockerfile
M test/docker/base/run_test_wrapper.sh
A test/docker/base/selenium/LICENSE
A test/docker/base/selenium/README
A test/docker/base/selenium/entry_point.sh
A test/docker/base/selenium/functions.sh
A test/docker/base/selenium/generate_config
A test/docker/base/selenium/wrap_chrome_binary
M test/functional/test_toolbox.py
M test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/navigates_galaxy.py
M test/manual/workflows_scaling.py
M test/qunit/test-app.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/graph.js
M test/qunit/tests/hda-base.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/job-dag.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/masthead_tests.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/modal_tests.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/popover_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/utils_test.js
M test/qunit/tests/workflow_editor_tests.js
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_contents.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/twilltestcase.py
M test/unit/config/1607_root_filters/config/galaxy.ini
M test/unit/config/1607_root_samples/config/galaxy.ini
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
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_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.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_parsing.py
M test/unit/tools/test_select_parameters.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_watcher.py
M test/unit/tools_support.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.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 tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/phenotype_association/senatag.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into tdt_tests
Commit: 9273d7a1c73df1aeb2271dcad6495d1b6fd4f036
https://github.com/galaxyproject/galaxy/commit/9273d7a1c73df1aeb2271dcad649…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M test/selenium_tests/test_tool_describing_tours.py
Log Message:
-----------
Add screenshots for TDT Selenium tests.
Commit: fb91302458f1ab8c1d8dbd59ef0d7ebf29932536
https://github.com/galaxyproject/galaxy/commit/fb91302458f1ab8c1d8dbd59ef0d…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M config/plugins/webhooks/demo/tour_generator/static/script.js
Log Message:
-----------
Fix TDT fors ES6 module switchover.
Commit: 54c6a794e9c6c3b5e51990875516e026cbac94c0
https://github.com/galaxyproject/galaxy/commit/54c6a794e9c6c3b5e51990875516…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M config/plugins/webhooks/demo/tour_generator/static/script.js
M static/maps/mvc/tool/tool-form-base.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
A test/functional/webhooks/tour_generator
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
A test/selenium_tests/test_tool_describing_tours.py
M test/selenium_tests/test_tool_form.py
Log Message:
-----------
Merge pull request #4909 from anatskiy/tdt_tests
Selenium test for Tool-Describing-Tours
Compare: https://github.com/galaxyproject/galaxy/compare/a12b50c08ecf...54c6a794e9c6
1
0
15 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b4e041d14d4b036c0c6fac3565e92f265d62f079
https://github.com/galaxyproject/galaxy/commit/b4e041d14d4b036c0c6fac3565e9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M tox.ini
Log Message:
-----------
Removed unneeded skip_install tags in tox.ini.
Alternative to #4995 thanks to @nsoranzo's detective work.
Commit: a12b50c08ecffa383f97342ae53f874be20aff56
https://github.com/galaxyproject/galaxy/commit/a12b50c08ecffa383f97342ae53f…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M tox.ini
Log Message:
-----------
Merge pull request #5011 from jmchilton/remove_skip_install_tox
Removed unneeded skip_install tags in tox.ini.
Compare: https://github.com/galaxyproject/galaxy/compare/482ff776e596...a12b50c08ecf
1
0
[galaxyproject/galaxy] 68a83c: dataset info: present decoded IDs for admins and a...
by GitHub 15 Nov '17
by GitHub 15 Nov '17
15 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 68a83ce08395fabf9c388fd0d8fa84cd4ba85e85
https://github.com/galaxyproject/galaxy/commit/68a83ce08395fabf9c388fd0d8fa…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M templates/show_params.mako
Log Message:
-----------
dataset info: present decoded IDs for admins and add peek
Commit: 482ff776e59612a5130e8af45661e514764bb0b5
https://github.com/galaxyproject/galaxy/commit/482ff776e59612a5130e8af45661…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M templates/show_params.mako
Log Message:
-----------
Merge pull request #5006 from martenson/decode_for_admins
dataset info: present decoded IDs for admins and add peek
Compare: https://github.com/galaxyproject/galaxy/compare/39bd5c6a194a...482ff776e596
1
0