galaxy-commits
Threads by month
- ----- 2025 -----
- July
- June
- May
- April
- March
- February
- January
- ----- 2024 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2023 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2022 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2021 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2020 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2019 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2018 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2017 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2016 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2015 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2014 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2013 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2012 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2011 -----
- December
- November
- October
- September
- August
- July
- June
- May
- April
- March
- February
- January
- ----- 2010 -----
- December
- November
- October
- September
- August
- July
- June
- May
- 15302 discussions
08 Aug '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c2246d8b8a17fdf126aefb5f6b53eb680bb58848
https://github.com/galaxyproject/galaxy/commit/c2246d8b8a17fdf126aefb5f6b53…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-08 (Wed, 08 Aug 2018)
Changed paths:
M test/base/rules_test_data.py
Log Message:
-----------
Fix last consistently failing Selenium test.
Commit: 75e50d3fdd98a75cc0c109616293608bdab5eac3
https://github.com/galaxyproject/galaxy/commit/75e50d3fdd98a75cc0c109616293…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-08 (Wed, 08 Aug 2018)
Changed paths:
M test/base/rules_test_data.py
Log Message:
-----------
Merge pull request #6578 from jmchilton/selenium_fixes_44
Fix last consistently failing Selenium test.
Compare: https://github.com/galaxyproject/galaxy/compare/a7e159dd8b8c...75e50d3fdd98
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
[galaxyproject/galaxy] ec6032: Client rebuild to include uploadbox value fix in r...
by GitHub 08 Aug '18
by GitHub 08 Aug '18
08 Aug '18
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: ec60327f983ced46fa2a8489c359100960b72d5b
https://github.com/galaxyproject/galaxy/commit/ec60327f983ced46fa2a8489c359…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Client rebuild to include uploadbox value fix in release branch.
Commit: d7398672a1a3432ae11b0c41b291e45e77bbd183
https://github.com/galaxyproject/galaxy/commit/d7398672a1a3432ae11b0c41b291…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-08 (Wed, 08 Aug 2018)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/utils/uploadbox.js
Log Message:
-----------
Merge pull request #6574 from dannon/release_18.05
[18.05] Client rebuild to include uploadbox value fix in release branch.
Compare: https://github.com/galaxyproject/galaxy/compare/f992980d458e...d7398672a1a3
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
[galaxyproject/galaxy] 4f3cd8: Typo and wording fixes for dependency resolvers do...
by GitHub 07 Aug '18
by GitHub 07 Aug '18
07 Aug '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4f3cd889f1cb2371519cabbc975dfffee6ec9b71
https://github.com/galaxyproject/galaxy/commit/4f3cd889f1cb2371519cabbc975d…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
Log Message:
-----------
Typo and wording fixes for dependency resolvers docs
Commit: a7e159dd8b8c584772defb6becb56f5450172dad
https://github.com/galaxyproject/galaxy/commit/a7e159dd8b8c584772defb6becb5…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M doc/source/admin/conda_faq.rst
M doc/source/admin/dependency_resolvers.rst
Log Message:
-----------
Merge pull request #6575 from afgane/dev
Typo and wording fixes for dependency resolvers docs
Compare: https://github.com/galaxyproject/galaxy/compare/55436c38008c...a7e159dd8b8c
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
07 Aug '18
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 1d0f51a05e5e5fb73940d7dae284bf9c00a4054c
https://github.com/galaxyproject/galaxy/commit/1d0f51a05e5e5fb73940d7dae284…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
Log Message:
-----------
Fix upload file selector value resetting
Fix
Commit: f992980d458edeebc0501ac036c2ee5c6fba7989
https://github.com/galaxyproject/galaxy/commit/f992980d458edeebc0501ac036c2…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M client/galaxy/scripts/utils/uploadbox.js
Log Message:
-----------
Merge pull request #6573 from guerler/fix_upload_naming
[18.05] Fix upload file selector value resetting
Compare: https://github.com/galaxyproject/galaxy/compare/ea085b07a0ef...f992980d458e
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: fa3a2371e1b2873456a3034874036d9b8cadd01c
https://github.com/galaxyproject/galaxy/commit/fa3a2371e1b2873456a303487403…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
WIP: add a SelectTagParameter
Commit: 4afbdbab31791101578be08acc3526e04c1835d6
https://github.com/galaxyproject/galaxy/commit/4afbdbab31791101578be08acc35…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M test/unit/test_objectstore.py
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Fix unit tests
Commit: 04b0cfcc1388de18aeb93a39fa44451009bbd67f
https://github.com/galaxyproject/galaxy/commit/04b0cfcc1388de18aeb93a39fa44…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-07 (Wed, 07 Feb 2018)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Make `get_datasets_for_group` case insensitive to tag
Commit: 45b2b7f434fc1bd1e646c72c6024bacc482a8b8e
https://github.com/galaxyproject/galaxy/commit/45b2b7f434fc1bd1e646c72c6024…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-24 (Tue, 24 Jul 2018)
Changed paths:
M .ci/check_py3_compatibility.sh
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M .ci/flake8_wrapper_docstrings.sh
M .ci/jenkins/selenium/run_tests.sh
M .gitignore
M .travis.yml
M CONTRIBUTING.md
M Makefile
M README.rst
M client/.babelrc
M client/GruntFile.js
M client/README.md
M client/bower.json
A client/galaxy/docs/bootstrap.md
A client/galaxy/docs/galaxy-buttons.md
A client/galaxy/docs/galaxy-forms.md
A client/galaxy/docs/galaxy-masthead.md
A client/galaxy/docs/galaxy-menus.md
A client/galaxy/docs/galaxy-messages.md
A client/galaxy/docs/galaxy-panels.md
A client/galaxy/docs/galaxy-tables.md
A client/galaxy/docs/galaxy-tabs.md
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/chart.js
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/components/Citations.vue
A client/galaxy/scripts/components/DataDialog.vue
A client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryImport.vue
A client/galaxy/scripts/components/HistoryView.vue
A client/galaxy/scripts/components/PluginList.vue
A client/galaxy/scripts/components/RuleCollectionBuilder.vue
A client/galaxy/scripts/components/RulesDisplay.vue
A client/galaxy/scripts/components/Sharing.vue
A client/galaxy/scripts/components/WorkflowImport.vue
M client/galaxy/scripts/components/admin/DataTablesGrid.vue
A client/galaxy/scripts/components/admin/DataTypes.vue
R client/galaxy/scripts/components/admin/UserAPIKeys.vue
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.pages.js
A client/galaxy/scripts/layout/communication-server-view.js
A client/galaxy/scripts/layout/data.js
R 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/scratchbook.js
M client/galaxy/scripts/legacy/grid/grid-view.js
R client/galaxy/scripts/libs/bootstrap-tour.js
R client/galaxy/scripts/libs/bootstrap.js
A client/galaxy/scripts/mocha/test.js
A client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml
A client/galaxy/scripts/mocha/tests/rules_tests.js
M client/galaxy/scripts/mvc/collection/collection-model.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-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-model.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-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/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/history-contents.js
M 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
R client/galaxy/scripts/mvc/history/history-structure-view.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/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.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-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/list/list-view.js
A client/galaxy/scripts/mvc/rules/rule-definitions.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/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/ui-buttons.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
A client/galaxy/scripts/mvc/ui/ui-rules-edit.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-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-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
A client/galaxy/scripts/mvc/upload/collection/rules-input-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-ftp.js
A client/galaxy/scripts/mvc/upload/upload-utils.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-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
A client/galaxy/scripts/mvc/visualization/chart/chart-client.js
A client/galaxy/scripts/mvc/visualization/chart/components/model.js
A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
A client/galaxy/scripts/mvc/visualization/chart/views/description.js
A client/galaxy/scripts/mvc/visualization/chart/views/editor.js
A client/galaxy/scripts/mvc/visualization/chart/views/groups.js
A client/galaxy/scripts/mvc/visualization/chart/views/menu.js
A client/galaxy/scripts/mvc/visualization/chart/views/settings.js
A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
M client/galaxy/scripts/mvc/visualization/visualization-model.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-manager.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
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/reports/run_stats.js
M client/galaxy/scripts/toolshed/groups/group-detail-view.js
M client/galaxy/scripts/toolshed/groups/group-list-view.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
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/visualization.js
R client/galaxy/style/less/autocomplete_tagging.less
R client/galaxy/style/less/base.less
R client/galaxy/style/less/bootstrap.less
R client/galaxy/style/less/bootstrap/alerts.less
R client/galaxy/style/less/bootstrap/badges.less
R client/galaxy/style/less/bootstrap/bootstrap.less
R client/galaxy/style/less/bootstrap/breadcrumbs.less
R client/galaxy/style/less/bootstrap/button-groups.less
R client/galaxy/style/less/bootstrap/buttons.less
R client/galaxy/style/less/bootstrap/carousel.less
R client/galaxy/style/less/bootstrap/close.less
R client/galaxy/style/less/bootstrap/code.less
R client/galaxy/style/less/bootstrap/component-animations.less
R client/galaxy/style/less/bootstrap/dropdowns.less
R client/galaxy/style/less/bootstrap/forms.less
R client/galaxy/style/less/bootstrap/glyphicons.less
R client/galaxy/style/less/bootstrap/grid.less
R client/galaxy/style/less/bootstrap/input-groups.less
R client/galaxy/style/less/bootstrap/jumbotron.less
R client/galaxy/style/less/bootstrap/labels.less
R client/galaxy/style/less/bootstrap/list-group.less
R client/galaxy/style/less/bootstrap/media.less
R client/galaxy/style/less/bootstrap/mixins.less
R client/galaxy/style/less/bootstrap/modals.less
R client/galaxy/style/less/bootstrap/navbar.less
R client/galaxy/style/less/bootstrap/navs.less
R client/galaxy/style/less/bootstrap/normalize.less
R client/galaxy/style/less/bootstrap/pager.less
R client/galaxy/style/less/bootstrap/pagination.less
R client/galaxy/style/less/bootstrap/panels.less
R client/galaxy/style/less/bootstrap/popovers.less
R client/galaxy/style/less/bootstrap/print.less
R client/galaxy/style/less/bootstrap/progress-bars.less
R client/galaxy/style/less/bootstrap/responsive-utilities.less
R client/galaxy/style/less/bootstrap/scaffolding.less
R client/galaxy/style/less/bootstrap/tables.less
R client/galaxy/style/less/bootstrap/theme.less
R client/galaxy/style/less/bootstrap/thumbnails.less
R client/galaxy/style/less/bootstrap/tooltip.less
R client/galaxy/style/less/bootstrap/type.less
R client/galaxy/style/less/bootstrap/utilities.less
R client/galaxy/style/less/bootstrap/variables.less
R client/galaxy/style/less/bootstrap/wells.less
R client/galaxy/style/less/circster.less
R client/galaxy/style/less/collection.less
R client/galaxy/style/less/dataset.less
R client/galaxy/style/less/embed_item.less
R client/galaxy/style/less/flex.less
R client/galaxy/style/less/fontawesome/bordered-pulled.less
R client/galaxy/style/less/fontawesome/core.less
R client/galaxy/style/less/fontawesome/fixed-width.less
R client/galaxy/style/less/fontawesome/font-awesome.less
R client/galaxy/style/less/fontawesome/icons.less
R client/galaxy/style/less/fontawesome/larger.less
R client/galaxy/style/less/fontawesome/list.less
R client/galaxy/style/less/fontawesome/mixins.less
R client/galaxy/style/less/fontawesome/path.less
R client/galaxy/style/less/fontawesome/rotated-flipped.less
R client/galaxy/style/less/fontawesome/spinning.less
R client/galaxy/style/less/fontawesome/stacked.less
R client/galaxy/style/less/fontawesome/variables.less
R client/galaxy/style/less/frame.less
R client/galaxy/style/less/galaxy_bootstrap.less
R client/galaxy/style/less/galaxy_bootstrap/overrides.less
R client/galaxy/style/less/galaxy_bootstrap/variables.less
R client/galaxy/style/less/galaxy_variables.less
R client/galaxy/style/less/history.less
R client/galaxy/style/less/iconic_stroke.less
R client/galaxy/style/less/job.less
R client/galaxy/style/less/jstree.less
R client/galaxy/style/less/library.less
R client/galaxy/style/less/list-item.less
R client/galaxy/style/less/reports.less
R client/galaxy/style/less/select2.less
R client/galaxy/style/less/theme/blue.less
R client/galaxy/style/less/theme/plain.less
R client/galaxy/style/less/toastr.less
R client/galaxy/style/less/tour.less
R client/galaxy/style/less/trackster.less
R client/galaxy/style/less/ui.less
R client/galaxy/style/less/ui/dataset-choice.less
R client/galaxy/style/less/ui/error-modal.less
R client/galaxy/style/less/ui/icon-btn.less
R client/galaxy/style/less/ui/pagination.less
R client/galaxy/style/less/ui/paired-collection-creator.less
R client/galaxy/style/less/ui/peek-column-selector.less
R client/galaxy/style/less/ui/search-input.less
R client/galaxy/style/less/upload.less
A client/galaxy/style/scss/autocomplete_tagging.scss
A client/galaxy/style/scss/base.scss
A client/galaxy/style/scss/charts.scss
A client/galaxy/style/scss/circster.scss
A client/galaxy/style/scss/collection.scss
A client/galaxy/style/scss/dataset.scss
A client/galaxy/style/scss/embed_item.scss
A client/galaxy/style/scss/flex.scss
A client/galaxy/style/scss/frame.scss
A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss
A client/galaxy/style/scss/galaxy_bootstrap/variables.scss
A client/galaxy/style/scss/galaxy_variables.scss
A client/galaxy/style/scss/history.scss
A client/galaxy/style/scss/iconic_stroke.scss
A client/galaxy/style/scss/job.scss
A client/galaxy/style/scss/jstree.scss
A client/galaxy/style/scss/library.scss
A client/galaxy/style/scss/list-item.scss
A client/galaxy/style/scss/reports.scss
A client/galaxy/style/scss/select2.scss
A client/galaxy/style/scss/theme/blue.scss
A client/galaxy/style/scss/theme/plain.scss
A client/galaxy/style/scss/toastr.scss
A client/galaxy/style/scss/tour.scss
A client/galaxy/style/scss/trackster.scss
A client/galaxy/style/scss/ui.scss
A client/galaxy/style/scss/ui/dataset-choice.scss
A client/galaxy/style/scss/ui/error-modal.scss
A client/galaxy/style/scss/ui/icon-btn.scss
A client/galaxy/style/scss/ui/pagination.scss
A client/galaxy/style/scss/ui/paired-collection-creator.scss
A client/galaxy/style/scss/ui/peek-column-selector.scss
A client/galaxy/style/scss/ui/search-input.scss
A client/galaxy/style/scss/upload.scss
R client/grunt-tasks/style.js
M client/gulpfile.js
M client/karma.config.js
M client/package.json
A client/styleguide.config.js
M client/webpack.config.js
M client/yarn.lock
M config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/job_conf.xml.sample_basic
M config/job_metrics_conf.xml.sample
M config/local_conda_mapping.yml.sample
A config/oidc_backends_config.xml.sample
A config/oidc_config.xml.sample
M config/openid_conf.xml.sample
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/tours/core.scratchbook.yaml
R config/plugins/visualizations/charts/config/charts.xml
R config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/static/client/app.css
R config/plugins/visualizations/charts/static/client/app.js
R config/plugins/visualizations/charts/static/client/components/model.js
R config/plugins/visualizations/charts/static/client/components/screenshot.js
R config/plugins/visualizations/charts/static/client/views/description.js
R config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/groups.js
R config/plugins/visualizations/charts/static/client/views/settings.js
R config/plugins/visualizations/charts/static/client/views/viewer.js
R config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
R config/plugins/visualizations/charts/static/repository/build/others_example.js
R config/plugins/visualizations/charts/static/repository/build/others_example.js.map
R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/registry.js
R config/plugins/visualizations/charts/static/repository/build/registry.js.map
R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
R config/plugins/visualizations/charts/static/repository/registry.json
R config/plugins/visualizations/charts/static/repository/utilities/jobs.js
R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
R config/plugins/visualizations/charts/static/repository/utilities/utils.js
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/templates/charts.mako
R config/plugins/visualizations/charts/webpack.config.js
A config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/common/templates/script_entry_point.mako
M config/plugins/visualizations/csg/config/csg.xml
A config/plugins/visualizations/csg/static/logo.png
M config/plugins/visualizations/csg/templates/csg.mako
A config/plugins/visualizations/cytoscape/config/cytoscape.xml
A config/plugins/visualizations/cytoscape/package.json
A config/plugins/visualizations/cytoscape/src/script.js
A config/plugins/visualizations/cytoscape/static/logo.png
A config/plugins/visualizations/cytoscape/static/script.js
A config/plugins/visualizations/drawrna/config/drawrna.xml
A config/plugins/visualizations/drawrna/package.json
A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js
A config/plugins/visualizations/drawrna/src/script.js
A config/plugins/visualizations/drawrna/static/logo.png
A config/plugins/visualizations/drawrna/static/script.js
A config/plugins/visualizations/example/config/example.xml
A config/plugins/visualizations/example/package.json
A config/plugins/visualizations/example/src/script.js
A config/plugins/visualizations/example/static/logo.png
A config/plugins/visualizations/example/static/script.js
M config/plugins/visualizations/graphviz/config/graphviz.xml
R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js
R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js
R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png
A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml
A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml
A config/plugins/visualizations/heatmap/heatmap_default/package.json
A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js
A config/plugins/visualizations/heatmap/heatmap_default/src/script.js
A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png
A config/plugins/visualizations/heatmap/heatmap_default/static/script.js
A config/plugins/visualizations/hivtrace/config/hivtrace.xml
A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2
A config/plugins/visualizations/hivtrace/static/674f50d287a8c48dc19ba404d20fe713.eot
A config/plugins/visualizations/hivtrace/static/89889688147bd7575d6327160d64e760.svg
A config/plugins/visualizations/hivtrace/static/912ec66d7572ff821749319396470bde.svg
A config/plugins/visualizations/hivtrace/static/af7ae505a9eed503f8b8e6982036873e.woff2
A config/plugins/visualizations/hivtrace/static/b06871f281fee6b241d60582ae9369b9.ttf
A config/plugins/visualizations/hivtrace/static/e18bbf611f2a2e43afc071aa2f4e1512.ttf
A config/plugins/visualizations/hivtrace/static/f4769f9bdb7466be65088239c12046d1.eot
A config/plugins/visualizations/hivtrace/static/fa2772327f55d8198301fdb8bcfc8158.woff
A config/plugins/visualizations/hivtrace/static/fee66e712a8a08eef5805a46892932ad.woff
A config/plugins/visualizations/hivtrace/static/hivtrace.css
A config/plugins/visualizations/hivtrace/static/hivtrace.css.map
A config/plugins/visualizations/hivtrace/static/hivtrace.js
A config/plugins/visualizations/hivtrace/static/hivtrace.js.map
A config/plugins/visualizations/hivtrace/static/logo.png
A config/plugins/visualizations/hivtrace/static/vendor.js
A config/plugins/visualizations/hivtrace/static/vendor.js.map
A config/plugins/visualizations/hivtrace/templates/index.mako
A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml
A config/plugins/visualizations/jqplot/jqplot_bar/package.json
A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js
A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css
A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js
A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png
A config/plugins/visualizations/msa/config/msa.xml
A config/plugins/visualizations/msa/package.json
A config/plugins/visualizations/msa/src/msa.js
A config/plugins/visualizations/msa/static/logo.png
A config/plugins/visualizations/msa/static/script.js
A config/plugins/visualizations/ngl/config/ngl.xml
A config/plugins/visualizations/ngl/package.json
A config/plugins/visualizations/ngl/src/ngl.js
A config/plugins/visualizations/ngl/src/viewer.js
A config/plugins/visualizations/ngl/static/logo.png
A config/plugins/visualizations/ngl/static/ngl.js
A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc
A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml
A config/plugins/visualizations/nvd3/nvd3_bar/package.json
A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js
A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css
A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png
A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml
A config/plugins/visualizations/phylocanvas/package.json
A config/plugins/visualizations/phylocanvas/src/script.js
A config/plugins/visualizations/phylocanvas/static/logo.png
A config/plugins/visualizations/phylocanvas/static/script.js
M config/plugins/visualizations/phyloviz/config/phyloviz.xml
A config/plugins/visualizations/phyloviz/static/logo.png
A config/plugins/visualizations/pv/config/pv.xml
A config/plugins/visualizations/pv/package.json
A config/plugins/visualizations/pv/src/pv.js
A config/plugins/visualizations/pv/static/logo.png
A config/plugins/visualizations/pv/static/pv.js
A config/plugins/visualizations/scatterplot/.babelrc
M config/plugins/visualizations/scatterplot/config/scatterplot.xml
M config/plugins/visualizations/scatterplot/package.json
A config/plugins/visualizations/scatterplot/src/jqglobals.js
A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js
M config/plugins/visualizations/scatterplot/src/scatterplot.js
A config/plugins/visualizations/scatterplot/src/worker-stats.js
A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js
A config/plugins/visualizations/scatterplot/static/logo.png
R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js
A config/plugins/visualizations/scatterplot/static/scatterplot.js
R config/plugins/visualizations/scatterplot/static/worker-stats.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
R config/plugins/visualizations/scatterplot/webpack.config.js
M config/plugins/visualizations/trackster/config/trackster.xml
A config/plugins/visualizations/trackster/static/logo.png
M config/plugins/visualizations/unipept/config/unipept.xml
M config/plugins/visualizations/unipept/templates/unipept.mako
A config/plugins/visualizations/venn/config/venn.xml
A config/plugins/visualizations/venn/package.json
A config/plugins/visualizations/venn/src/script.js
A config/plugins/visualizations/venn/src/venn.js
A config/plugins/visualizations/venn/static/logo.png
A config/plugins/visualizations/venn/static/script.css
A config/plugins/visualizations/venn/static/script.js
M config/plugins/webhooks/demo/search/script.js
M config/plugins/webhooks/demo/tour_generator/__init__.py
M config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
M config/tool_destinations.yml.sample
M config/tool_shed.yml.sample
M config/user_preferences_extra_conf.yml.sample
A config/workflow_resource_mapper_conf.yml.sample
A config/workflow_resource_params_conf.xml.sample
M create_db.sh
M display_applications/igb/bam.xml
M display_applications/igb/bb.xml
M display_applications/igb/bed.xml
M display_applications/igb/bedgraph.xml
M display_applications/igb/bigwig.xml
M display_applications/igb/gtf.xml
M display_applications/igb/wig.xml
A display_applications/intermine/intermine_simple.xml
M doc/parse_gx_xsd.py
M doc/source/admin/authentication.md
M doc/source/admin/cluster.md
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/nginx.md
M doc/source/admin/reports_options.rst
M doc/source/admin/scaling.md
M doc/source/admin/special_topics/bug_reports.rst
A doc/source/admin/special_topics/gdpr_compliance.rst
M doc/source/admin/special_topics/index.rst
M doc/source/admin/special_topics/performance_tracking.rst
M doc/source/conf.py
A doc/source/conf.versioning.py
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/project/organization.rst
A doc/source/releases/18.01.rst
M doc/source/releases/18.01_announce.rst
A doc/source/releases/18.05.rst
A doc/source/releases/18.05_announce.rst
M doc/source/releases/index.rst
M extract_dataset_parts.sh
M lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
M lib/galaxy/auth/providers/pam_auth.py
A lib/galaxy/authnz/__init__.py
A lib/galaxy/authnz/managers.py
A lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/containers/docker_swarm.py
R lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
A lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_fai.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml
R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml
R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml
R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml
R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml
R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml
R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml
R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml
R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
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_fli.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
R lib/galaxy/datatypes/converters/sam_to_bam_native.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
A lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml
A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.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/1.afg
A lib/galaxy/datatypes/test/1.arff
A lib/galaxy/datatypes/test/1.fastqsanger.bz2
A lib/galaxy/datatypes/test/1.fastqsanger.gz
A lib/galaxy/datatypes/test/1.genbank
A lib/galaxy/datatypes/test/1.genbank.gz
A lib/galaxy/datatypes/test/1.hdt
A lib/galaxy/datatypes/test/1.obo
A lib/galaxy/datatypes/test/1.owl
A lib/galaxy/datatypes/test/1.phyloxml
A lib/galaxy/datatypes/test/1.stockholm
A lib/galaxy/datatypes/test/1.tiff
A lib/galaxy/datatypes/test/1.ttl
A lib/galaxy/datatypes/test/1.xmfa
A lib/galaxy/datatypes/test/2.tabular
A lib/galaxy/datatypes/test/2.txt
A lib/galaxy/datatypes/test/3.txt
A lib/galaxy/datatypes/test/Acanium.hmm
A lib/galaxy/datatypes/test/diamond.daa
A lib/galaxy/datatypes/test/empty.txt
M lib/galaxy/datatypes/test/example.iqtree
A lib/galaxy/datatypes/test/test.blib
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/triples.py
A lib/galaxy/datatypes/upload_util.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/conditional-requirements.txt
R lib/galaxy/dependencies/pinned-hashed-requirements.txt
A lib/galaxy/dependencies/pinned-requirements.txt
R lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/default/Pipfile
A lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
R lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
R lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/dynamic_tool_destination.py
R lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
A lib/galaxy/jobs/metrics/instrumenters/cgroup.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
A lib/galaxy/jobs/metrics/instrumenters/hostname.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/torque.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
R lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
R lib/galaxy/jobs/runners/util/retry.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
A lib/galaxy/managers/cloud.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py
A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
M lib/galaxy/model/orm/engine_factory.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/tools/apply_rules.xml
M lib/galaxy/tools/cwl/__init__.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
A lib/galaxy/tools/cwl/util.py
M lib/galaxy/tools/data/__init__.py
A lib/galaxy/tools/data_fetch.py
A lib/galaxy/tools/data_fetch.xml
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.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/docker_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_files.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/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/lmod.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/deps/views.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/filter_empty_collection.xml
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/linters/command.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/cwl.py
A lib/galaxy/tools/parser/error_level.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/util.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/repositories.py
M lib/galaxy/tools/special_tools.py
A lib/galaxy/tools/tag_collection_from_file.xml
M lib/galaxy/tools/test.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/asserts/__init__.py
A lib/galaxy/tools/verify/interactor.py
A lib/galaxy/tools/verify/script.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
A lib/galaxy/util/create_history_template.py
M lib/galaxy/util/facts.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/json.py
M lib/galaxy/util/monitors.py
M lib/galaxy/util/none_like.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/permutations.py
A lib/galaxy/util/rules_dsl.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/script.py
M lib/galaxy/util/validation.py
A lib/galaxy/util/watcher.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/helpers/grids.py
A lib/galaxy/web/framework/helpers/tags.py
M lib/galaxy/web/framework/middleware/batch.py
R lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/sentry.py
A lib/galaxy/web/framework/middleware/sqldebug.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/web/security/__init__.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/config_manage.py
A lib/galaxy/webapps/galaxy/api/_fetch_util.py
M lib/galaxy/webapps/galaxy/api/annotations.py
A lib/galaxy/webapps/galaxy/api/cloud.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
A lib/galaxy/webapps/galaxy/api/plugins.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/tools.py
A lib/galaxy/webapps/galaxy/api/uploads.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
A lib/galaxy/webapps/galaxy/controllers/authnz.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/config_schema.yml
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.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/model/__init__.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/modules.py
A lib/galaxy/workflow/resources/__init__.py
A lib/galaxy/workflow/resources/example.py.sample
M lib/galaxy/workflow/run_request.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.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/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.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/admin_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/web_util.py
M lib/tool_shed/util/workflow_util.py
M manage_db.sh
R openid/aol.xml
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/common.py
A scripts/api/fetch_to_library.py
A scripts/api/fetch_to_library_example.yml
A scripts/apply_tags.py
M scripts/bootstrap_history.py
M scripts/check_python.py
M scripts/cleanup_datasets/admin_cleanup_datasets.py
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/delete_datasets.sh
M scripts/cleanup_datasets/delete_userless_histories.sh
M scripts/cleanup_datasets/pgcleanup.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/purge_datasets.sh
M scripts/cleanup_datasets/purge_folders.sh
M scripts/cleanup_datasets/purge_histories.sh
M scripts/cleanup_datasets/purge_libraries.sh
R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
R scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
R scripts/common_startup_variables.sh
M scripts/communication/communication_server.py
R scripts/data_libraries/build_lucene_index.py
R scripts/data_libraries/build_lucene_index.sh
R scripts/data_libraries/build_whoosh_index.py
R scripts/data_libraries/build_whoosh_index.sh
M scripts/db_shell.py
A scripts/docker_swarm_manager.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
M scripts/grt/upload.py
M scripts/helper.py
M scripts/maintenance.sh
M scripts/manage_db.py
R scripts/microbes/BeautifulSoup.py
M scripts/microbes/harvest_bacteria.py
M scripts/migrate_tools/migrate_tools.py
R scripts/others/incorrect_gops_jobs.py
R scripts/others/incorrect_gops_jobs.sh
R scripts/others/incorrect_gops_join_jobs.py
R scripts/others/incorrect_gops_join_jobs.sh
A scripts/plugin_staging.py
M scripts/runtime_stats.py
M scripts/secret_decoder_ring.py
M scripts/set_dataset_sizes.py
M scripts/set_user_disk_usage.py
M scripts/sync_reports_config.py
M scripts/transfer.py
A static/images/fonts/FontAwesome.otf
M static/images/fonts/fontawesome-webfont.eot
A static/images/fonts/fontawesome-webfont.svg
M static/images/fonts/fontawesome-webfont.ttf
M static/images/fonts/fontawesome-webfont.woff
A static/images/fonts/fontawesome-webfont.woff2
R static/scripts/admin.toolshed.js
R static/scripts/bundled/admin.bundled.js
R static/scripts/bundled/analysis.bundled.js
R static/scripts/bundled/extended.bundled.js
R static/scripts/bundled/libs.bundled.js
R static/scripts/bundled/login.bundled.js
R static/scripts/galaxy.interactive_environments.js
R static/scripts/galaxy.js
R static/scripts/galaxy.library.js
R static/scripts/galaxy.pages.js
R static/scripts/i18n.js
R static/scripts/layout/generic-nav-view.js
R static/scripts/layout/masthead.js
R static/scripts/layout/menu.js
R static/scripts/layout/modal.js
R static/scripts/layout/page.js
R static/scripts/layout/panel.js
R static/scripts/layout/router.js
R static/scripts/layout/scratchbook.js
R static/scripts/legacy/grid/grid-model.js
R static/scripts/legacy/grid/grid-template.js
R static/scripts/legacy/grid/grid-view.js
R static/scripts/libs/backbone.js
R static/scripts/libs/bbi/bigwig.js
R static/scripts/libs/bbi/jquery-ajax-native.js
R static/scripts/libs/bbi/jszlib.js
R static/scripts/libs/bbi/spans.js
R static/scripts/libs/bibtexParse.js
R static/scripts/libs/bootstrap-tour.js
R static/scripts/libs/bootstrap.js
R static/scripts/libs/d3.js
R static/scripts/libs/farbtastic.js
R static/scripts/libs/jquery.sparklines.js
R static/scripts/libs/jquery/jquery-ui.js
R static/scripts/libs/jquery/jquery.autocomplete.js
R static/scripts/libs/jquery/jquery.complexify.js
R static/scripts/libs/jquery/jquery.cookie.js
R static/scripts/libs/jquery/jquery.dynatree.js
R static/scripts/libs/jquery/jquery.event.drag.js
R static/scripts/libs/jquery/jquery.event.drop.js
R static/scripts/libs/jquery/jquery.event.hover.js
R static/scripts/libs/jquery/jquery.form.js
R static/scripts/libs/jquery/jquery.js
R static/scripts/libs/jquery/jquery.migrate.js
R static/scripts/libs/jquery/jquery.mousewheel.js
R static/scripts/libs/jquery/jquery.rating.js
R static/scripts/libs/jquery/jquery.wymeditor.js
R static/scripts/libs/jquery/jstorage.js
R static/scripts/libs/jquery/jstree.js
R static/scripts/libs/jquery/select2.js
R static/scripts/libs/raven.js
R static/scripts/libs/require.js
R static/scripts/libs/toastr.js
R static/scripts/libs/underscore.js
R static/scripts/mvc/annotation.js
R static/scripts/mvc/base-mvc.js
R static/scripts/mvc/base/controlled-fetch-collection.js
R static/scripts/mvc/collection/base-creator.js
R static/scripts/mvc/collection/collection-li-edit.js
R static/scripts/mvc/collection/collection-li.js
R static/scripts/mvc/collection/collection-model.js
R static/scripts/mvc/collection/collection-view-edit.js
R static/scripts/mvc/collection/collection-view.js
R static/scripts/mvc/collection/list-collection-creator.js
R static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R static/scripts/mvc/collection/pair-collection-creator.js
R static/scripts/mvc/dataset/data.js
R static/scripts/mvc/dataset/dataset-choice.js
R static/scripts/mvc/dataset/dataset-edit-attributes.js
R static/scripts/mvc/dataset/dataset-error.js
R static/scripts/mvc/dataset/dataset-li-edit.js
R static/scripts/mvc/dataset/dataset-li.js
R static/scripts/mvc/dataset/dataset-list.js
R static/scripts/mvc/dataset/dataset-model.js
R static/scripts/mvc/dataset/states.js
R static/scripts/mvc/form/form-data.js
R static/scripts/mvc/form/form-input.js
R static/scripts/mvc/form/form-parameters.js
R static/scripts/mvc/form/form-repeat.js
R static/scripts/mvc/form/form-section.js
R static/scripts/mvc/form/form-view.js
R static/scripts/mvc/form/form-wrapper.js
R static/scripts/mvc/grid/grid-model.js
R static/scripts/mvc/grid/grid-shared.js
R static/scripts/mvc/grid/grid-template.js
R static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/history/copy-dialog.js
R static/scripts/mvc/history/hda-li-edit.js
R static/scripts/mvc/history/hda-li.js
R static/scripts/mvc/history/hda-model.js
R static/scripts/mvc/history/hdca-li-edit.js
R static/scripts/mvc/history/hdca-li.js
R static/scripts/mvc/history/hdca-model.js
R static/scripts/mvc/history/history-content-model.js
R static/scripts/mvc/history/history-contents.js
R static/scripts/mvc/history/history-item-li.js
R static/scripts/mvc/history/history-list.js
R static/scripts/mvc/history/history-model.js
R static/scripts/mvc/history/history-preferences.js
R static/scripts/mvc/history/history-structure-view.js
R static/scripts/mvc/history/history-view-annotated.js
R static/scripts/mvc/history/history-view-edit-current.js
R static/scripts/mvc/history/history-view-edit.js
R static/scripts/mvc/history/history-view.js
R static/scripts/mvc/history/job-dag.js
R static/scripts/mvc/history/job-states-model.js
R static/scripts/mvc/history/multi-panel.js
R static/scripts/mvc/history/options-menu.js
R static/scripts/mvc/job/job-li.js
R static/scripts/mvc/job/job-model.js
R static/scripts/mvc/job/job-params.js
R static/scripts/mvc/lazy/lazy-limited.js
R static/scripts/mvc/library/library-dataset-view.js
R static/scripts/mvc/library/library-folder-view.js
R static/scripts/mvc/library/library-folderlist-view.js
R static/scripts/mvc/library/library-folderrow-view.js
R static/scripts/mvc/library/library-foldertoolbar-view.js
R static/scripts/mvc/library/library-library-view.js
R static/scripts/mvc/library/library-librarylist-view.js
R static/scripts/mvc/library/library-libraryrow-view.js
R static/scripts/mvc/library/library-librarytoolbar-view.js
R static/scripts/mvc/library/library-model.js
R static/scripts/mvc/library/library-util.js
R static/scripts/mvc/list/list-item.js
R static/scripts/mvc/list/list-view.js
R static/scripts/mvc/tag.js
R static/scripts/mvc/tool/tool-form-base.js
R static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form.js
R static/scripts/mvc/tool/tool-genomespace.js
R static/scripts/mvc/tool/tools.js
R static/scripts/mvc/toolshed/categories-view.js
R static/scripts/mvc/toolshed/repo-queue-view.js
R static/scripts/mvc/toolshed/repo-status-view.js
R static/scripts/mvc/toolshed/repositories-view.js
R static/scripts/mvc/toolshed/repository-queue-view.js
R static/scripts/mvc/toolshed/repository-view.js
R static/scripts/mvc/toolshed/shed-list-view.js
R static/scripts/mvc/toolshed/toolshed-model.js
R static/scripts/mvc/toolshed/util.js
R static/scripts/mvc/toolshed/workflows-view.js
R static/scripts/mvc/tours.js
R static/scripts/mvc/ui/error-modal.js
R static/scripts/mvc/ui/icon-button.js
R static/scripts/mvc/ui/popup-menu.js
R static/scripts/mvc/ui/ui-buttons.js
R static/scripts/mvc/ui/ui-color-picker.js
R static/scripts/mvc/ui/ui-drilldown.js
R static/scripts/mvc/ui/ui-frames.js
R static/scripts/mvc/ui/ui-list.js
R static/scripts/mvc/ui/ui-misc.js
R static/scripts/mvc/ui/ui-modal.js
R static/scripts/mvc/ui/ui-options.js
R static/scripts/mvc/ui/ui-popover.js
R static/scripts/mvc/ui/ui-portlet.js
R static/scripts/mvc/ui/ui-select-content.js
R static/scripts/mvc/ui/ui-select-default.js
R static/scripts/mvc/ui/ui-select-ftp.js
R static/scripts/mvc/ui/ui-select-genomespace.js
R static/scripts/mvc/ui/ui-select-library.js
R static/scripts/mvc/ui/ui-select.js
R static/scripts/mvc/ui/ui-slider.js
R static/scripts/mvc/ui/ui-table.js
R static/scripts/mvc/ui/ui-tabs.js
R static/scripts/mvc/ui/ui-thumbnails.js
R static/scripts/mvc/upload/collection/collection-row.js
R static/scripts/mvc/upload/collection/collection-view.js
R static/scripts/mvc/upload/composite/composite-row.js
R static/scripts/mvc/upload/composite/composite-view.js
R static/scripts/mvc/upload/default/default-row.js
R static/scripts/mvc/upload/default/default-view.js
R static/scripts/mvc/upload/upload-button.js
R static/scripts/mvc/upload/upload-extension.js
R static/scripts/mvc/upload/upload-ftp.js
R static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-settings.js
R static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/user-custom-builds.js
R static/scripts/mvc/user/user-model.js
R static/scripts/mvc/user/user-preferences.js
R static/scripts/mvc/user/user-quotameter.js
R static/scripts/mvc/visualization/visualization-model.js
R static/scripts/mvc/webhooks.js
R static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-connector.js
R static/scripts/mvc/workflow/workflow-forms.js
R static/scripts/mvc/workflow/workflow-icons.js
R static/scripts/mvc/workflow/workflow-manager.js
R static/scripts/mvc/workflow/workflow-model.js
R static/scripts/mvc/workflow/workflow-node.js
R static/scripts/mvc/workflow/workflow-terminals.js
R static/scripts/mvc/workflow/workflow-view-data.js
R static/scripts/mvc/workflow/workflow-view-node.js
R static/scripts/mvc/workflow/workflow-view-terminals.js
R static/scripts/mvc/workflow/workflow-view.js
R static/scripts/mvc/workflow/workflow.js
R static/scripts/nls/de/locale.js
R static/scripts/nls/es/locale.js
R static/scripts/nls/fr/locale.js
R static/scripts/nls/ja/locale.js
R static/scripts/nls/locale.js
R static/scripts/nls/zh/locale.js
R static/scripts/onload.js
R static/scripts/packed
R static/scripts/polyfills.js
R static/scripts/reports/run_stats.js
R static/scripts/toolshed/groups/group-detail-view.js
R static/scripts/toolshed/groups/group-list-view.js
R static/scripts/toolshed/groups/group-listrow-view.js
R static/scripts/toolshed/groups/group-model.js
R static/scripts/toolshed/toolshed.groups.js
R static/scripts/ui/autocom_tagging.js
R static/scripts/ui/editable-text.js
R static/scripts/ui/fa-icon-button.js
R static/scripts/ui/filter-control.js
R static/scripts/ui/hoverhighlight.js
R static/scripts/ui/loading-indicator.js
R static/scripts/ui/mode-button.js
R static/scripts/ui/pagination.js
R static/scripts/ui/peek-column-selector.js
R static/scripts/ui/popupmenu.js
R static/scripts/ui/scroll-panel.js
R static/scripts/ui/search-input.js
R static/scripts/utils/add-logging.js
R static/scripts/utils/ajax-queue.js
R static/scripts/utils/async-save-text.js
R static/scripts/utils/config.js
R static/scripts/utils/deferred.js
R static/scripts/utils/graph.js
R static/scripts/utils/levenshtein.js
R static/scripts/utils/localization.js
R static/scripts/utils/metrics-logger.js
R static/scripts/utils/natural-sort.js
R static/scripts/utils/query-string-parsing.js
R static/scripts/utils/uploadbox.js
R static/scripts/utils/utils.js
R static/scripts/viz/bbi-data-manager.js
R static/scripts/viz/circster.js
R static/scripts/viz/phyloviz.js
R static/scripts/viz/sweepster.js
R static/scripts/viz/trackster.js
R static/scripts/viz/trackster/filters.js
R static/scripts/viz/trackster/painters.js
R static/scripts/viz/trackster/slotting.js
R static/scripts/viz/trackster/tracks.js
R static/scripts/viz/trackster/util.js
R static/scripts/viz/visualization.js
R static/scripts/viz/viz_views.js
M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/circster.css
M static/style/blue/embed_item.css
M static/style/blue/library.css
M static/style/blue/reports.css
M static/style/blue/trackster.css
M static/welcome.html.sample
R templates/admin/impersonate.mako
R templates/admin/view_data_tables_registry.mako
R templates/admin/view_datatypes_registry.mako
M templates/base/base_panels.mako
M templates/display_common.mako
M templates/ind_share_base.mako
M templates/js-app.mako
R templates/sharing_base.mako
M templates/show_params.mako
M templates/tagging_common.mako
M templates/user/login.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
R templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/structure.mako
R templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/galaxy/workflow/sharing.mako
M templates/webapps/reports/index.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/user/manage_email_alerts.mako
A test-data/1.csv
A test-data/1.tiff
A test-data/11.tabular
A test-data/configfile.json
A test-data/example-bag.zip
A test-data/filter1_in6.bed
A test-data/filter1_test6.bed
A test-data/new_tags_1.txt
A test-data/qname_sorted.bam
A test-data/rules/PRJDA60709.tsv
A test-data/rules/PRJDB3920.tsv
A test-data/rules/PRJNA355367.tsv
A test-data/rules/treated1fb.txt
A test-data/rules/treated2fb.txt
A test-data/rules/treated3fb.txt
A test-data/rules/uniprot.json
A test-data/rules/uniprot.tsv
A test-data/rules/untreated1fb.txt
A test-data/rules/untreated2fb.txt
A test-data/rules/untreated3fb.txt
A test-data/rules/untreated4fb.txt
A test-data/sort_out1.bed
A test-data/sort_out2.bed
A test-data/sort_out3.tab
A test-data/sort_out4.sam
A test-data/testdir1.zip
M test/api/test_dataset_collections.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_tools_upload.py
M test/api/test_visualizations.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/api.py
A test/base/data/rules_dsl_spec.yml
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/interactor.py
M test/base/populators.py
A test/base/rules_test_data.py
M test/base/testcase.py
R test/base/tool_shed_util.py
A test/base/workflow_fixtures.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
R test/casperjs/README.txt
R test/casperjs/api-anon-history-permission-tests.js
R test/casperjs/api-anon-history-tests.js
R test/casperjs/api-hda-tests.js
R test/casperjs/api-history-permission-tests.js
R test/casperjs/casperjs_runner.py
R test/casperjs/modules/api.js
R test/casperjs/modules/historyoptions.js
R test/casperjs/modules/historypanel.js
R test/casperjs/modules/tools.js
R test/casperjs/modules/user.js
R test/casperjs/page-data/selectors.json
R test/casperjs/server_env.py
R test/casperjs/spaceghost.js
R test/casperjs/test-data/simple_test.ga
R test/casperjs/utils/simple-galaxy.js
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
A test/functional/tools/collection_paired_conditional_structured_like.xml
A test/functional/tools/collection_paired_structured_like.xml
A test/functional/tools/collection_type_source_map_over.xml
A test/functional/tools/column_param_configfile.xml
A test/functional/tools/empty_select.xml
A test/functional/tools/fail_writing_work_dir_file.xml
M test/functional/tools/for_workflows/cat_collection.xml
A test/functional/tools/identifier_single_in_repeat.xml
A test/functional/tools/inputs_as_json_with_paths.xml
M test/functional/tools/job_properties.xml
M test/functional/tools/multi_data_optional.xml
M test/functional/tools/multi_output_recurse.xml
A test/functional/tools/output_action_change_format_paired.xml
R test/functional/tools/paired_collection_map_over_structured_like.xml
R test/functional/tools/sam_to_bam_native.xml
A test/functional/tools/sam_to_unsorted_bam.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/twilltestcase.py
M test/galaxy_selenium/components.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/galaxy_selenium/smart_components.py
M test/integration/test_data_manager_table_reload.py
A test/integration/test_scripts.py
A test/integration/test_shed_tool_tests.py
M test/integration/test_upload_configuration_options.py
A test/integration/uses_shed.py
R test/selenium_tests/_workflow_fixtures.py
M test/selenium_tests/framework.py
A test/selenium_tests/test_admin_app.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_library_to_collections.py
M test/selenium_tests/test_registration.py
M test/selenium_tests/test_saved_histories.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/twilltestcase.py
M test/shed_functional/test_data/emboss/datatypes/datatypes_conf.xml
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/test_bam.py
A test/unit/datatypes/test_datatypes_registry.py
A test/unit/jobs/dynamic_tool_destination/data/job_conf.xml
M test/unit/jobs/dynamic_tool_destination/data/priority_tool_destination.yml
M test/unit/jobs/dynamic_tool_destination/data/test_no_verbose.yml
M test/unit/jobs/dynamic_tool_destination/data/test_num_input_datasets.yml
M test/unit/jobs/dynamic_tool_destination/data/tool_destination.yml
M test/unit/jobs/dynamic_tool_destination/mockGalaxy.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/dynamic_tool_destination/ymltests.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_runner_params.py
M test/unit/managers/test_HistoryManager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_remote_shell.py
A test/unit/test_rule_utils.py
M test/unit/test_security_helper.py
A test/unit/test_security_passwords.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_validation.py
M test/unit/tools/test_toolbox.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.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_extract_summary.py
M test/unit/workflows/test_modules.py
A tool-data/intermine_simple_display.loc.sample
A tools/data_source/intermine.xml
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/cutWrapper.pl
M tools/filters/sorter.py
M tools/filters/sorter.xml
M tools/filters/wig_to_bigwig.xml
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_importer.xml
M tools/genomespace/genomespace_push.xml
M tools/phenotype_association/gpass.xml
M tools/phenotype_association/lps.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
M tools/sr_mapping/bfast_wrapper.xml
M tools/stats/filtering.py
M tools/stats/filtering.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into select_tag_parameter
Commit: d417e9b239309707274011d4199b8f827fcc0f6d
https://github.com/galaxyproject/galaxy/commit/d417e9b239309707274011d4199b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-24 (Tue, 24 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/api/test_tools.py
A test/functional/tools/collection_cat_group_tag.xml
A test/functional/tools/collection_cat_group_tag_multiple.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Flush out collection tag parameters a bit.
- Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data.
- Add minimal XSD documentation for this new parameter type.
- Add example tools - for single and multiple tags.
- Add API tests for these tools and the tag handling.
Commit: e5c532298d5db34da04d8f046ebe44abddbbaa64
https://github.com/galaxyproject/galaxy/commit/e5c532298d5db34da04d8f046ebe…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Make tag order stable when using group_tag parameters.
Commit: 6677e7b91385d027989613bdc621108da76e8425
https://github.com/galaxyproject/galaxy/commit/6677e7b91385d027989613bdc621…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths:
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Fix failing import/export test for group_tag changes.
Commit: 5a914b9fa71ff2c00d7ba1a7c1dc3ccbb8437eae
https://github.com/galaxyproject/galaxy/commit/5a914b9fa71ff2c00d7ba1a7c1dc…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Keep all user-selected tags, including duplicates
Commit: 95e8a3491280cc26d435bebc1cf03488d7db3b88
https://github.com/galaxyproject/galaxy/commit/95e8a3491280cc26d435bebc1cf0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Correct copy-pasted docstring
Commit: 55436c38008c3d1b261b7d9dfc728cc968bd6622
https://github.com/galaxyproject/galaxy/commit/55436c38008c3d1b261b7d9dfc72…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-08-07 (Tue, 07 Aug 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M test/api/test_tools.py
A test/functional/tools/collection_cat_group_tag.xml
A test/functional/tools/collection_cat_group_tag_multiple.xml
M test/functional/tools/samples_tool_conf.xml
M test/unit/test_objectstore.py
M test/unit/tools/test_wrappers.py
Log Message:
-----------
Merge pull request #5457 from mvdbeek/select_tag_parameter
Allow selecting subset of collection by group tag
Compare: https://github.com/galaxyproject/galaxy/compare/d1423b6e18cb...55436c38008c
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
07 Aug '18
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: 676886195d1fbe17cdff16af8acad6f5c2115ee1
https://github.com/galaxyproject/galaxy/commit/676886195d1fbe17cdff16af8aca…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-28 (Mon, 28 May 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix non-strict tabular relabel operation
Commit: 3b3deb314f4a78684bea9707d2f0d856e306f006
https://github.com/galaxyproject/galaxy/commit/3b3deb314f4a78684bea9707d2f0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-05-31 (Thu, 31 May 2018)
Changed paths:
M lib/galaxy/tools/relabel_from_file.xml
Log Message:
-----------
Use strict mode when testing strict mode ...
Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168
https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-02 (Sat, 02 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Allow invalid optional param values for old tools
For tools with profile < 18.09 we return None for provided, but illegal
default values. This can happen when referencing columns of an optional
dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842.
This used to pass prior to 18.05 because we would always return the
value if there were no legal values. This was changed in
https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f…
where we would only allow this in workflow building mode.
Commit: 470299a2ce6ef1e5d894a0247bd43f24fd463d41
https://github.com/galaxyproject/galaxy/commit/470299a2ce6ef1e5d894a0247bd4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-18 (Mon, 18 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
Log Message:
-----------
Merge pull request #6234 from mvdbeek/fix_relabel_non_strict
[18.01] Fix non-strict tabular relabel operation
Commit: eed703eef8b3884f70019070210633f0e033b39b
https://github.com/galaxyproject/galaxy/commit/eed703eef8b3884f700190702106…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-19 (Tue, 19 Jun 2018)
Changed paths:
M templates/sharing_base.mako
Log Message:
-----------
Fix share with another user in 18.05
Commit: 48fafa8096fd179e9c74c56bac7be9b042cbade8
https://github.com/galaxyproject/galaxy/commit/48fafa8096fd179e9c74c56bac7b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-19 (Tue, 19 Jun 2018)
Changed paths:
M templates/sharing_base.mako
Log Message:
-----------
Merge pull request #6358 from dannon/1805sharingfix
[18.01] Fix 'share with another user'
Commit: c6403acd0f18196c0453a90fe89ccf861d7a28d6
https://github.com/galaxyproject/galaxy/commit/c6403acd0f18196c0453a90fe89c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/output_collect.py
Log Message:
-----------
Fix logging bug.
Commit: d0a0fa8319e5b32e222e261b1b9f0242e210d1c7
https://github.com/galaxyproject/galaxy/commit/d0a0fa8319e5b32e222e261b1b9f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/relabel_from_file.xml
M templates/sharing_base.mako
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: 6d5be41b320510d6e2d163399a3a6e30d6f9bda0
https://github.com/galaxyproject/galaxy/commit/6d5be41b320510d6e2d163399a3a…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-06-20 (Wed, 20 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/output_collect.py
Log Message:
-----------
Merge pull request #6366 from jmchilton/job_log_bug
[18.05] Fix small bug in logging output name in job finish.
Commit: 603b2365b6a261e5603c618c637cf8458e667007
https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations
Commit: 572f38d1fb47e914ad10766007c855786e1643a2
https://github.com/galaxyproject/galaxy/commit/572f38d1fb47e914ad10766007c8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M scripts/grt/export.py
Log Message:
-----------
move the sanitization to the try/except block
as it may fail (and it did, on Main)
Commit: f94a073e86be608916ec7ae79285da06ee82483b
https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Make sure that the workflow step has a proper state available
Commit: d28ab2a4f31b363c236a02a535cc43ab049190ca
https://github.com/galaxyproject/galaxy/commit/d28ab2a4f31b363c236a02a535cc…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M scripts/grt/export.py
Log Message:
-----------
Merge pull request #6377 from martenson/catch-sanitization-faults
[18.05] Catch sanitization faults
Commit: 9967639bac92eb3f7103794663f41b88f11baa9c
https://github.com/galaxyproject/galaxy/commit/9967639bac92eb3f7103794663f4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Comma-separate tool names in missing tools error message
Commit: 22d383c39842e0a0198cf2d37ad3832ea1838769
https://github.com/galaxyproject/galaxy/commit/22d383c39842e0a0198cf2d37ad3…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M lib/galaxy/managers/workflows.py
Log Message:
-----------
Merge pull request #6378 from guerler/commaseperror
[18.05] Comma-separate tool names in missing tools error message
Commit: fa2b6baef71984c0559c53ff5750d1fe9b77163e
https://github.com/galaxyproject/galaxy/commit/fa2b6baef71984c0559c53ff5750…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/bam_to_bai.xml
Log Message:
-----------
Revert "Remove bam to bai converter"
This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb.
Commit: 5f24794efdad757b77c75c3aa111da7a11c5bb47
https://github.com/galaxyproject/galaxy/commit/5f24794efdad757b77c75c3aa111…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Add basic .bai datatype
Commit: 36706e9eb38728c91c1da2a4cf66ff49f3f44d72
https://github.com/galaxyproject/galaxy/commit/36706e9eb38728c91c1da2a4cf66…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-06-22 (Fri, 22 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/bam_to_bai.xml
Log Message:
-----------
Merge pull request #6385 from dannon/revert-baiconverter-removal
[18.01] Revert "Remove bam to bai converter"
Commit: e0c269291a20ae3a01a24bae930012baba3bb10c
https://github.com/galaxyproject/galaxy/commit/e0c269291a20ae3a01a24bae9300…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-06-23 (Sat, 23 Jun 2018)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/bam_to_bai.xml
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: 6654a837527797971b28fd2cbb092d7081c918b9
https://github.com/galaxyproject/galaxy/commit/6654a837527797971b28fd2cbb09…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-01 (Sun, 01 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Hack around #6299.
Commit: 39d7cf2eb73177532237ad38a8a75095d1be4428
https://github.com/galaxyproject/galaxy/commit/39d7cf2eb73177532237ad38a8a7…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-07-01 (Sun, 01 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #6433 from jmchilton/hack_6299
[18.05] decode potential encoded id
Commit: 0c97d4ff5c83318551319524582619656ae848b8
https://github.com/galaxyproject/galaxy/commit/0c97d4ff5c833185513195245826…
Author: thobalose <lose.thoba(a)gmail.com>
Date: 2018-07-04 (Wed, 04 Jul 2018)
Changed paths:
M lib/galaxy/visualization/plugins/interactive_environments.py
Log Message:
-----------
GIE static url; https://github.com/galaxyproject/galaxy/issues/6459
Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e
https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-07-05 (Thu, 05 Jul 2018)
Changed paths:
M lib/galaxy/visualization/plugins/interactive_environments.py
Log Message:
-----------
Merge pull request #6465 from dannon/backport-gie-static-again
[18.05] Backport of IE static url fix (to actual 18.05)
Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea
https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d…
Author: Devon Ryan <dpryan79(a)gmail.com>
Date: 2018-07-09 (Mon, 09 Jul 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Fix the --log-file option in the job handlers
(cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768)
Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa
https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge pull request #6477 from natefoo/backport-pr-6351
[18.01] Fix the --log-file option in the job handlers
Commit: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e
https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Merge pull request #6369 from guerler/pages
[18.05] Make sure that the workflow step has a proper state available
Commit: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0
https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Merge pull request #6375 from dannon/sentry_transport_fix
[18.05] Specify standard HTTPTransport for Sentry
Commit: 4b0ae30a83aeb86a821ec15cfa87e6af7e160a03
https://github.com/galaxyproject/galaxy/commit/4b0ae30a83aeb86a821ec15cfa87…
Author: takadonet <philipmabon(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Added fix to ensure that original ftp files that have been uploaded are purged if set in galaxy.yml with flag ftp_upload_purge. Address issue #6492
Commit: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106
https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-13 (Fri, 13 Jul 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: fd33c5c6d6aa2478654da74c7e80efdcf31e09a7
https://github.com/galaxyproject/galaxy/commit/fd33c5c6d6aa2478654da74c7e80…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-07-13 (Fri, 13 Jul 2018)
Changed paths:
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #6497 from martenson/backport-takadonet
[18.05] backport ftp purge fix
Commit: 7b8e4f9e740725861951535d59e50243e4a0b2e0
https://github.com/galaxyproject/galaxy/commit/7b8e4f9e740725861951535d59e5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/empty.txt
Log Message:
-----------
Fix empty datatypes.
Commit: ef702e1458f746299710e9ce5afb7b350b61f91c
https://github.com/galaxyproject/galaxy/commit/ef702e1458f746299710e9ce5afb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-07-17 (Tue, 17 Jul 2018)
Changed paths:
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/empty.txt
Log Message:
-----------
Merge pull request #6510 from nsoranzo/release_18.05_backport_29f8e29b0bf5d50c0b735aa707d2a61623cc805b
[18.05] Fix infinite loop in uploads
Commit: a8b9899681939286a03badd85c9c71f972958a18
https://github.com/galaxyproject/galaxy/commit/a8b9899681939286a03badd85c9c…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-23 (Mon, 23 Jul 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
Log Message:
-----------
Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
Since v2.27.0 (see
https://github.com/arq5x/bedtools2/commit/4d188435777cfbd6ada7394ee78fde37f… ),
`bedtools genomecov` emits this warning:
```
*****
*****WARNING: Genome (-g) files are ignored when BAM input is provided.
*****
```
if both `-ibam` and `-g` option are specified, which causes the converters to
always fail.
Also:
- Add `detect_errors="aggressive"` to `<command/>` to prevent future warnings from
creating other issues.
- Fix input format in `CONVERTER_sam_to_bigwig_0`.
Commit: 50b34185394cc38159c33ca98b74e1418a7b1e55
https://github.com/galaxyproject/galaxy/commit/50b34185394cc38159c33ca98b74…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-23 (Mon, 23 Jul 2018)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
Log Message:
-----------
Merge pull request #6528 from nsoranzo/release_18.05_fix_CONVERTER_bam_to_bigwig_0
[18.05] Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
Commit: 9794d835e507c31d82aa82c79e86998154419980
https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M test/api/test_tools.py
Log Message:
-----------
Fix to_dict with io_details=True for tools with collection outputs.
Fixes #6537 and includes a test case.
Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b
https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/util/rules_dsl.py
M test/unit/test_rule_utils.py
Log Message:
-----------
Fix empty handling rule.
Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8
https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values
[18.05] Allow invalid optional param values for tools profile versions < 18.09
Commit: 0a9010156e30a20d730324807c3e238510f44b77
https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #6538 from jmchilton/tool_output_io
[18.01] Fix to_dict with io_details=True for tools with collection outputs.
Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb
https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-30 (Mon, 30 Jul 2018)
Changed paths:
M lib/galaxy/util/rules_dsl.py
M test/unit/test_rule_utils.py
Log Message:
-----------
Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend
[18.05] Fix "filter empty" rule in Python rule handling framework.
Commit: 9630699c21875199fec75bc3f607d5b81a224348
https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-31 (Tue, 31 Jul 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev)
Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b
https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Introduce test for auto-labelling subworkflow workflow outputs
Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75
https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use subworkflow index when setting auto-label
Previously this would reference the parent workflow index, while the
get_data module would use the subworkflow index. This means defining
workflows worked fine, but executing would fail when trying to find the
output to replace. Using the subworkflow index here seems like the
correct thing to do.
Fixes https://github.com/galaxyproject/galaxy/issues/6560
Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e
https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Fix worklfow run link for extracted workflows
Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd
https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
Merge pull request #6532 from dannon/fix-dataset-copy-tags
[18.05] Fix dataset copy tags
Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94
https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery
[18.01] Use subworkflow index when setting auto-label
Commit: d7959568f85b45f378f6972d971075f7169cffc4
https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d9710…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5
https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613f…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #6571 from guerler/fix_link
[18.05] Fix workflow run link for extracted workflows
Compare: https://github.com/galaxyproject/galaxy/compare/bcf105cbb37a...ea085b07a0ef
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
[galaxyproject/galaxy] 4661b6: Allow invalid optional param values for old tools
by GitHub 07 Aug '18
by GitHub 07 Aug '18
07 Aug '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4661b6e8831c2cae86b7d9725431e71bacd22168
https://github.com/galaxyproject/galaxy/commit/4661b6e8831c2cae86b7d9725431…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-06-02 (Sat, 02 Jun 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Allow invalid optional param values for old tools
For tools with profile < 18.09 we return None for provided, but illegal
default values. This can happen when referencing columns of an optional
dataset for instance, as experienced in https://github.com/galaxyproject/tools-iuc/pull/1842.
This used to pass prior to 18.05 because we would always return the
value if there were no legal values. This was changed in
https://github.com/galaxyproject/galaxy/commit/9febc519944dcfb5c8907b8a302f…
where we would only allow this in workflow building mode.
Commit: 9794d835e507c31d82aa82c79e86998154419980
https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M test/api/test_tools.py
Log Message:
-----------
Fix to_dict with io_details=True for tools with collection outputs.
Fixes #6537 and includes a test case.
Commit: 5f19b8752dfd940efd156de1a0c1a4e6e914800b
https://github.com/galaxyproject/galaxy/commit/5f19b8752dfd940efd156de1a0c1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/util/rules_dsl.py
M test/unit/test_rule_utils.py
Log Message:
-----------
Fix empty handling rule.
Commit: a88bf0a2bee152c859f229c2a017b8a03d96b8d8
https://github.com/galaxyproject/galaxy/commit/a88bf0a2bee152c859f229c2a017…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Merge pull request #6264 from mvdbeek/allow_optional_and_invalid_parameter_values
[18.05] Allow invalid optional param values for tools profile versions < 18.09
Commit: 0a9010156e30a20d730324807c3e238510f44b77
https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #6538 from jmchilton/tool_output_io
[18.01] Fix to_dict with io_details=True for tools with collection outputs.
Commit: 66e74d0e475ef6fd6f6de125b41f9990e274fbfb
https://github.com/galaxyproject/galaxy/commit/66e74d0e475ef6fd6f6de125b41f…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-07-30 (Mon, 30 Jul 2018)
Changed paths:
M lib/galaxy/util/rules_dsl.py
M test/unit/test_rule_utils.py
Log Message:
-----------
Merge pull request #6542 from jmchilton/1805_fix_empty_handling_rule_on_backend
[18.05] Fix "filter empty" rule in Python rule handling framework.
Commit: 9630699c21875199fec75bc3f607d5b81a224348
https://github.com/galaxyproject/galaxy/commit/9630699c21875199fec75bc3f607…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-07-31 (Tue, 31 Jul 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
Simpler, more targeted fix for copy datasets dialog tag copies (will refactor in dev)
Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b
https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Introduce test for auto-labelling subworkflow workflow outputs
Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75
https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use subworkflow index when setting auto-label
Previously this would reference the parent workflow index, while the
get_data module would use the subworkflow index. This means defining
workflows worked fine, but executing would fail when trying to find the
output to replace. Using the subworkflow index here seems like the
correct thing to do.
Fixes https://github.com/galaxyproject/galaxy/issues/6560
Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e
https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Fix worklfow run link for extracted workflows
Commit: 6c7b9a3c7d4459b171fa806f2912d49e44ccd5bd
https://github.com/galaxyproject/galaxy/commit/6c7b9a3c7d4459b171fa806f2912…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/dataset.py
Log Message:
-----------
Merge pull request #6532 from dannon/fix-dataset-copy-tags
[18.05] Fix dataset copy tags
Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94
https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery
[18.01] Use subworkflow index when setting auto-label
Commit: d7959568f85b45f378f6972d971075f7169cffc4
https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d9710…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5
https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613f…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #6571 from guerler/fix_link
[18.05] Fix workflow run link for extracted workflows
Commit: d1423b6e18cbf054799027d6c6700b1b1186d6a9
https://github.com/galaxyproject/galaxy/commit/d1423b6e18cbf054799027d6c670…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/util/rules_dsl.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
M test/unit/test_rule_utils.py
Log Message:
-----------
Merge branch 'release_18.05' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/561e0099bc22...d1423b6e18cb
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
07 Aug '18
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: ffdf674c75d49235edee80090fe4235ac9b0d86e
https://github.com/galaxyproject/galaxy/commit/ffdf674c75d49235edee80090fe4…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Fix worklfow run link for extracted workflows
Commit: ea085b07a0efdd5322aab3bb613fc363b71967b5
https://github.com/galaxyproject/galaxy/commit/ea085b07a0efdd5322aab3bb613f…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #6571 from guerler/fix_link
[18.05] Fix workflow run link for extracted workflows
Compare: https://github.com/galaxyproject/galaxy/compare/d7959568f85b...ea085b07a0ef
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
[galaxyproject/galaxy] 9794d8: Fix to_dict with io_details=True for tools with co...
by GitHub 07 Aug '18
by GitHub 07 Aug '18
07 Aug '18
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 9794d835e507c31d82aa82c79e86998154419980
https://github.com/galaxyproject/galaxy/commit/9794d835e507c31d82aa82c79e86…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-25 (Wed, 25 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M test/api/test_tools.py
Log Message:
-----------
Fix to_dict with io_details=True for tools with collection outputs.
Fixes #6537 and includes a test case.
Commit: 0a9010156e30a20d730324807c3e238510f44b77
https://github.com/galaxyproject/galaxy/commit/0a9010156e30a20d730324807c3e…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-07-26 (Thu, 26 Jul 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #6538 from jmchilton/tool_output_io
[18.01] Fix to_dict with io_details=True for tools with collection outputs.
Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b
https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Introduce test for auto-labelling subworkflow workflow outputs
Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75
https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use subworkflow index when setting auto-label
Previously this would reference the parent workflow index, while the
get_data module would use the subworkflow index. This means defining
workflows worked fine, but executing would fail when trying to find the
output to replace. Using the subworkflow index here seems like the
correct thing to do.
Fixes https://github.com/galaxyproject/galaxy/issues/6560
Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94
https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery
[18.01] Use subworkflow index when setting auto-label
Commit: d7959568f85b45f378f6972d971075f7169cffc4
https://github.com/galaxyproject/galaxy/commit/d7959568f85b45f378f6972d9710…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Compare: https://github.com/galaxyproject/galaxy/compare/6c7b9a3c7d44...d7959568f85b
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0
[galaxyproject/galaxy] ba4718: Introduce test for auto-labelling subworkflow work...
by GitHub 07 Aug '18
by GitHub 07 Aug '18
07 Aug '18
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: ba47188f5e896d9f2bd6718796093f05e1c7aa9b
https://github.com/galaxyproject/galaxy/commit/ba47188f5e896d9f2bd671879609…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Introduce test for auto-labelling subworkflow workflow outputs
Commit: 21fd74e640c2ba872d98259ea213e20e99c6ba75
https://github.com/galaxyproject/galaxy/commit/21fd74e640c2ba872d98259ea213…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Use subworkflow index when setting auto-label
Previously this would reference the parent workflow index, while the
get_data module would use the subworkflow index. This means defining
workflows worked fine, but executing would fail when trying to find the
output to replace. Using the subworkflow index here seems like the
correct thing to do.
Fixes https://github.com/galaxyproject/galaxy/issues/6560
Commit: 6d9df51f36e293bd1ce20d3bf9e21a5646ff5b94
https://github.com/galaxyproject/galaxy/commit/6d9df51f36e293bd1ce20d3bf9e2…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-08-06 (Mon, 06 Aug 2018)
Changed paths:
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge pull request #6570 from mvdbeek/fix_auto_labelling_and_output_recovery
[18.01] Use subworkflow index when setting auto-label
Compare: https://github.com/galaxyproject/galaxy/compare/0a9010156e30...6d9df51f36e2
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
1
0