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December 2017
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[galaxyproject/galaxy] 743441: Rebuild fr locale.js file to match basic locale....
by GitHub 07 Dec '17
by GitHub 07 Dec '17
07 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 7434411e14039d035f3f2309f0ff1a5de7bdc498
https://github.com/galaxyproject/galaxy/commit/7434411e14039d035f3f2309f0ff…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
Log Message:
-----------
Rebuild fr locale.js file to match basic locale.js
Commit: 886aded175c7f870152305480856a8a8c287b3f8
https://github.com/galaxyproject/galaxy/commit/886aded175c7f870152305480856…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.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-repeat.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/icon-button.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-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/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/qunit/tests/modal_tests.js
M client/galaxy/scripts/qunit/tests/popover_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.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/tracks.js
M client/galaxy/scripts/viz/visualization.js
Log Message:
-----------
Add new title entries basic locale.js and fr
Commit: 3fba0d049ac589d1306c211cc59dd22f5ea1a40c
https://github.com/galaxyproject/galaxy/commit/3fba0d049ac589d1306c211cc59d…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
Log Message:
-----------
Add new description entries in basic locale.js and fr
Commit: a8fc967df2ff52aeaf9fb938aa16de79a40008e3
https://github.com/galaxyproject/galaxy/commit/a8fc967df2ff52aeaf9fb938aa16…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
Log Message:
-----------
Add new help entries in basic locale.js and fr
Commit: f8a5108d6db32917f9aaca73db6ac37643be765d
https://github.com/galaxyproject/galaxy/commit/f8a5108d6db32917f9aaca73db6a…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-11-29 (Wed, 29 Nov 2017)
Changed paths:
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Add new tooltip entries in basic locale.js and fr
Commit: b9461e32b8731eeb46b13271a5a10187a18e7632
https://github.com/galaxyproject/galaxy/commit/b9461e32b8731eeb46b13271a5a1…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.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-repeat.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/icon-button.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-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/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/qunit/tests/modal_tests.js
M client/galaxy/scripts/qunit/tests/popover_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.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/tracks.js
M client/galaxy/scripts/viz/visualization.js
Log Message:
-----------
remove labels entries and useless translation
Commit: 12f2f74db3ab29d3cbeaab9b4c1e6c05456c61b6
https://github.com/galaxyproject/galaxy/commit/12f2f74db3ab29d3cbeaab9b4c1e…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
Log Message:
-----------
Remove translation of name
Commit: 05aae3c69c8eb744d87931c632dc785d0b57166c
https://github.com/galaxyproject/galaxy/commit/05aae3c69c8eb744d87931c632dc…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M client/galaxy/scripts/qunit/tests/modal_tests.js
M client/galaxy/scripts/qunit/tests/popover_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
Log Message:
-----------
Drop changes in qunit files
Commit: 9d16aacfe1d069e8d41792494d49b9b99b89e158
https://github.com/galaxyproject/galaxy/commit/9d16aacfe1d069e8d41792494d49…
Author: ValentinChCloud <chavaldranis(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
Log Message:
-----------
Add and remove one comma
Commit: d042f446a4c27d1358c394ef485b71ef7c2b8134
https://github.com/galaxyproject/galaxy/commit/d042f446a4c27d1358c394ef485b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.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/form/form-repeat.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-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/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.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/tracks.js
M client/galaxy/scripts/viz/visualization.js
Log Message:
-----------
Merge pull request #5089 from ValentinChCloud/dev
i18n improvements French localization the sequel
Compare: https://github.com/galaxyproject/galaxy/compare/3a9d63c69005...d042f446a4c2
1
0
07 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 38ec399d56f07e40c64f37342b099fab65c746d7
https://github.com/galaxyproject/galaxy/commit/38ec399d56f07e40c64f37342b09…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix revision selection during installation
Without this the model would be refetched and would remain at the initial
changeset revision.
Commit: 7bbd2dbd758cf685978dee4deb50d047b648b9fe
https://github.com/galaxyproject/galaxy/commit/7bbd2dbd758cf685978dee4deb50…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Order the metadata revisions
Commit: 41e2558ed5d228cd4b5b3c45b59d80ff7dcb7f8b
https://github.com/galaxyproject/galaxy/commit/41e2558ed5d228cd4b5b3c45b59d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Fix undefined variable error in repository installation queue
Commit: fd16b3d3b46dde3d11ab357704755915149cb8d8
https://github.com/galaxyproject/galaxy/commit/fd16b3d3b46dde3d11ab35770475…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message:
-----------
Fix key error for non-tool workflow steps (i.e collection input)
Commit: 39912e8c5beba8daa82078aa3a9626cedded5277
https://github.com/galaxyproject/galaxy/commit/39912e8c5beba8daa82078aa3a96…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M static/maps/mvc/toolshed/repository-view.js.map
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Add static JS
Commit: d95ad427618ae6dae88c58e5eaed29aa7e16393b
https://github.com/galaxyproject/galaxy/commit/d95ad427618ae6dae88c58e5eaed…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/toolshed.py
Log Message:
-----------
Fix KeyError in beta repository installation
Repository metadata may not include tool dependencies.
Commit: ec81d16585e43335cd54d4d5c3f415e861db6522
https://github.com/galaxyproject/galaxy/commit/ec81d16585e43335cd54d4d5c3f4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
R .ci/flake8_lint_include_list.txt
R .ci/flake8_wrapper_imports.sh
M .ci/jenkins/selenium/run_tests.sh
M .gitignore
M .travis.yml
M Makefile
M README.rst
M client/README.md
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
A client/galaxy/scripts/components/Citations.vue
A client/galaxy/scripts/components/HistoryImport.vue
A client/galaxy/scripts/components/UserAPIKeys.vue
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/i18n.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/mvc/annotation.js
R client/galaxy/scripts/mvc/citation/citation-model.js
R client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.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/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
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M lib/galaxy/datatypes/mothur.py
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M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
R lib/galaxy/webapps/galaxy/controllers/library_admin.py
R lib/galaxy/webapps/galaxy/controllers/library_common.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/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/config.py
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/controllers/user.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/schedulers/core.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/utility_containers/__init__.py
R manage_tools.sh
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/display.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
M scripts/db_shell.py
M scripts/functional_tests.py
M scripts/galaxy-main
A scripts/get_uwsgi_args.py
M scripts/manage_tool_dependencies.py
R scripts/manage_tools.py
M scripts/microbes/harvest_bacteria.py
R static/GruntFile.js.map
R static/maps/admin.toolshed.js.map
R static/maps/analysis.js.map
R static/maps/app.js.map
R static/maps/app/analysis.js.map
R static/maps/galaxy-app-base.js.map
R static/maps/galaxy.interactive_environments.js.map
R static/maps/galaxy.js.map
R static/maps/galaxy.library.js.map
R static/maps/galaxy.menu.js.map
R static/maps/galaxy.pages.js.map
R static/maps/i18n.js.map
R static/maps/layout/generic-nav-view.js.map
R static/maps/layout/masthead.js.map
R static/maps/layout/menu.js.map
R static/maps/layout/modal.js.map
R static/maps/layout/page.js.map
R static/maps/layout/panel.js.map
R static/maps/layout/router.js.map
R static/maps/layout/scratchbook.js.map
R static/maps/libs/backbone.js.map
R static/maps/libs/bbi/bigwig.js.map
R static/maps/libs/bbi/jquery-ajax-native.js.map
R static/maps/libs/bbi/jszlib.js.map
R static/maps/libs/bbi/spans.js.map
R static/maps/libs/bibtex.js.map
R static/maps/libs/bootstrap-tour.js.map
R static/maps/libs/bootstrap.js.map
R static/maps/libs/common-libs.js.map
R static/maps/libs/d3.js.map
R static/maps/libs/farbtastic.js.map
R static/maps/libs/jquery.complexify.js.map
R static/maps/libs/jquery.sparklines.js.map
R static/maps/libs/jquery/jquery-ui.js.map
R static/maps/libs/jquery/jquery.autocomplete.js.map
R static/maps/libs/jquery/jquery.complexify.js.map
R static/maps/libs/jquery/jquery.cookie.js.map
R static/maps/libs/jquery/jquery.dynatree.js.map
R static/maps/libs/jquery/jquery.event.drag.js.map
R static/maps/libs/jquery/jquery.event.drop.js.map
R static/maps/libs/jquery/jquery.event.hover.js.map
R static/maps/libs/jquery/jquery.form.js.map
R static/maps/libs/jquery/jquery.js.map
R static/maps/libs/jquery/jquery.migrate.js.map
R static/maps/libs/jquery/jquery.mousewheel.js.map
R static/maps/libs/jquery/jquery.rating.js.map
R static/maps/libs/jquery/jquery.wymeditor.js.map
R static/maps/libs/jquery/jstorage.js.map
R static/maps/libs/jquery/jstree.js.map
R static/maps/libs/jquery/select2.js.map
R static/maps/libs/raven.js.map
R static/maps/libs/require.js.map
R static/maps/libs/showdown.js.map
R static/maps/libs/toastr.js.map
R static/maps/libs/underscore.js.map
R static/maps/mvc/annotation.js.map
R static/maps/mvc/base-mvc.js.map
R static/maps/mvc/base/controlled-fetch-collection.js.map
R static/maps/mvc/citation/citation-model.js.map
R static/maps/mvc/citation/citation-view.js.map
R static/maps/mvc/collection/base-creator.js.map
R static/maps/mvc/collection/collection-li-edit.js.map
R static/maps/mvc/collection/collection-li.js.map
R static/maps/mvc/collection/collection-model.js.map
R static/maps/mvc/collection/collection-view-edit.js.map
R static/maps/mvc/collection/collection-view.js.map
R static/maps/mvc/collection/list-collection-creator.js.map
R static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
R static/maps/mvc/collection/pair-collection-creator.js.map
R static/maps/mvc/collection/paired-collection-creator.js.map
R static/maps/mvc/dataset/data.js.map
R static/maps/mvc/dataset/dataset-choice.js.map
R static/maps/mvc/dataset/dataset-edit-attributes.js.map
R static/maps/mvc/dataset/dataset-error.js.map
R static/maps/mvc/dataset/dataset-li-edit.js.map
R static/maps/mvc/dataset/dataset-li.js.map
R static/maps/mvc/dataset/dataset-list.js.map
R static/maps/mvc/dataset/dataset-model.js.map
R static/maps/mvc/dataset/states.js.map
R static/maps/mvc/form/form-data.js.map
R static/maps/mvc/form/form-input.js.map
R static/maps/mvc/form/form-parameters.js.map
R static/maps/mvc/form/form-repeat.js.map
R static/maps/mvc/form/form-section.js.map
R static/maps/mvc/form/form-view.js.map
R static/maps/mvc/form/form-wrapper.js.map
R static/maps/mvc/grid/grid-model.js.map
R static/maps/mvc/grid/grid-shared.js.map
R static/maps/mvc/grid/grid-template.js.map
R static/maps/mvc/grid/grid-view.js.map
R static/maps/mvc/groups/group-detail-view.js.map
R static/maps/mvc/groups/group-groupdetail-view.js.map
R static/maps/mvc/groups/group-grouprow-view.js.map
R static/maps/mvc/groups/group-list-view.js.map
R static/maps/mvc/groups/group-listrow-view.js.map
R static/maps/mvc/groups/group-model.js.map
R static/maps/mvc/groups/group.model.js.map
R static/maps/mvc/history/copy-dialog.js.map
R static/maps/mvc/history/hda-li-edit.js.map
R static/maps/mvc/history/hda-li.js.map
R static/maps/mvc/history/hda-model.js.map
R static/maps/mvc/history/hdca-li-edit.js.map
R static/maps/mvc/history/hdca-li.js.map
R static/maps/mvc/history/hdca-model.js.map
R static/maps/mvc/history/history-content-model.js.map
R static/maps/mvc/history/history-contents.js.map
R static/maps/mvc/history/history-list.js.map
R static/maps/mvc/history/history-model.js.map
R static/maps/mvc/history/history-preferences.js.map
R static/maps/mvc/history/history-structure-view.js.map
R static/maps/mvc/history/history-view-annotated.js.map
R static/maps/mvc/history/history-view-edit-current.js.map
R static/maps/mvc/history/history-view-edit.js.map
R static/maps/mvc/history/history-view.js.map
R static/maps/mvc/history/job-dag.js.map
R static/maps/mvc/history/multi-panel.js.map
R static/maps/mvc/history/options-menu.js.map
R static/maps/mvc/job/job-li.js.map
R static/maps/mvc/job/job-model.js.map
R static/maps/mvc/job/job-params.js.map
R static/maps/mvc/lazy/lazy-limited.js.map
R static/maps/mvc/library/library-dataset-view.js.map
R static/maps/mvc/library/library-folder-view.js.map
R static/maps/mvc/library/library-folderlist-view.js.map
R static/maps/mvc/library/library-folderrow-view.js.map
R static/maps/mvc/library/library-foldertoolbar-view.js.map
R static/maps/mvc/library/library-library-view.js.map
R static/maps/mvc/library/library-librarylist-view.js.map
R static/maps/mvc/library/library-libraryrow-view.js.map
R static/maps/mvc/library/library-librarytoolbar-view.js.map
R static/maps/mvc/library/library-model.js.map
R static/maps/mvc/library/library-util.js.map
R static/maps/mvc/list/list-item.js.map
R static/maps/mvc/list/list-panel.js.map
R static/maps/mvc/list/list-view.js.map
R static/maps/mvc/page/page-list.js.map
R static/maps/mvc/tag.js.map
R static/maps/mvc/tool/tool-form-base.js.map
R static/maps/mvc/tool/tool-form-composite.js.map
R static/maps/mvc/tool/tool-form.js.map
R static/maps/mvc/tool/tool-genomespace.js.map
R static/maps/mvc/tool/tool-template.js.map
R static/maps/mvc/tool/tool-webhooks.js.map
R static/maps/mvc/tool/tools.js.map
R static/maps/mvc/toolshed/categories-view.js.map
R static/maps/mvc/toolshed/repo-queue-view.js.map
R static/maps/mvc/toolshed/repo-status-view.js.map
R static/maps/mvc/toolshed/repositories-view.js.map
R static/maps/mvc/toolshed/repository-queue-view.js.map
R static/maps/mvc/toolshed/repository-view.js.map
R static/maps/mvc/toolshed/shed-category-view.js.map
R static/maps/mvc/toolshed/shed-list-view.js.map
R static/maps/mvc/toolshed/shed-repo-details-view.js.map
R static/maps/mvc/toolshed/shed-repo-list-view.js.map
R static/maps/mvc/toolshed/sheds-list-view.js.map
R static/maps/mvc/toolshed/toolshed-model.js.map
R static/maps/mvc/toolshed/util.js.map
R static/maps/mvc/toolshed/workflows-view.js.map
R static/maps/mvc/tours.js.map
R static/maps/mvc/ui/error-modal.js.map
R static/maps/mvc/ui/icon-button.js.map
R static/maps/mvc/ui/popup-menu.js.map
R static/maps/mvc/ui/ui-buttons.js.map
R static/maps/mvc/ui/ui-color-picker.js.map
R static/maps/mvc/ui/ui-drilldown.js.map
R static/maps/mvc/ui/ui-frames.js.map
R static/maps/mvc/ui/ui-list.js.map
R static/maps/mvc/ui/ui-misc.js.map
R static/maps/mvc/ui/ui-modal.js.map
R static/maps/mvc/ui/ui-options.js.map
R static/maps/mvc/ui/ui-popover.js.map
R static/maps/mvc/ui/ui-portlet.js.map
R static/maps/mvc/ui/ui-select-content.js.map
R static/maps/mvc/ui/ui-select-default.js.map
R static/maps/mvc/ui/ui-select-ftp.js.map
R static/maps/mvc/ui/ui-select-genomespace.js.map
R static/maps/mvc/ui/ui-select-library.js.map
R static/maps/mvc/ui/ui-select.js.map
R static/maps/mvc/ui/ui-slider.js.map
R static/maps/mvc/ui/ui-table.js.map
R static/maps/mvc/ui/ui-tabs.js.map
R static/maps/mvc/ui/ui-thumbnails.js.map
R static/maps/mvc/upload/collection/collection-row.js.map
R static/maps/mvc/upload/collection/collection-view.js.map
R static/maps/mvc/upload/composite/composite-row.js.map
R static/maps/mvc/upload/composite/composite-view.js.map
R static/maps/mvc/upload/default/default-row.js.map
R static/maps/mvc/upload/default/default-view.js.map
R static/maps/mvc/upload/upload-button.js.map
R static/maps/mvc/upload/upload-extension.js.map
R static/maps/mvc/upload/upload-ftp.js.map
R static/maps/mvc/upload/upload-model.js.map
R static/maps/mvc/upload/upload-row.js.map
R static/maps/mvc/upload/upload-settings.js.map
R static/maps/mvc/upload/upload-view.js.map
R static/maps/mvc/user/change-password.js.map
R static/maps/mvc/user/extra-information.js.map
R static/maps/mvc/user/manage-user-information.js.map
R static/maps/mvc/user/user-custom-builds.js.map
R static/maps/mvc/user/user-model.js.map
R static/maps/mvc/user/user-preferences.js.map
R static/maps/mvc/user/user-quotameter.js.map
R static/maps/mvc/visualization/visualization-model.js.map
R static/maps/mvc/webhooks.js.map
R static/maps/mvc/workflow/workflow-canvas.js.map
R static/maps/mvc/workflow/workflow-configure-menu.js.map
R static/maps/mvc/workflow/workflow-connector.js.map
R static/maps/mvc/workflow/workflow-forms.js.map
R static/maps/mvc/workflow/workflow-icons.js.map
R static/maps/mvc/workflow/workflow-manager.js.map
R static/maps/mvc/workflow/workflow-model.js.map
R static/maps/mvc/workflow/workflow-node.js.map
R static/maps/mvc/workflow/workflow-terminals.js.map
R static/maps/mvc/workflow/workflow-view-data.js.map
R static/maps/mvc/workflow/workflow-view-node.js.map
R static/maps/mvc/workflow/workflow-view-terminals.js.map
R static/maps/mvc/workflow/workflow-view.js.map
R static/maps/mvc/workflow/workflow.js.map
R static/maps/nls/de/locale.js.map
R static/maps/nls/es/locale.js.map
R static/maps/nls/fr/locale.js.map
R static/maps/nls/ja/locale.js.map
R static/maps/nls/locale.js.map
R static/maps/nls/zh/locale.js.map
R static/maps/onload.js.map
R static/maps/polyfills.js.map
R static/maps/reports_webapp/run_stats.js.map
R static/maps/templates/compiled/panel_section.js.map
R static/maps/templates/compiled/tool_form.js.map
R static/maps/templates/compiled/tool_link.js.map
R static/maps/templates/compiled/tool_search.js.map
R static/maps/toolshed.groups.js.map
R static/maps/ui/autocom_tagging.js.map
R static/maps/ui/editable-text.js.map
R static/maps/ui/fa-icon-button.js.map
R static/maps/ui/filter-control.js.map
R static/maps/ui/hoverhighlight.js.map
R static/maps/ui/loading-indicator.js.map
R static/maps/ui/mode-button.js.map
R static/maps/ui/pagination.js.map
R static/maps/ui/peek-column-selector.js.map
R static/maps/ui/popupmenu.js.map
R static/maps/ui/scroll-panel.js.map
R static/maps/ui/search-input.js.map
R static/maps/utils/add-logging.js.map
R static/maps/utils/ajax-queue.js.map
R static/maps/utils/async-save-text.js.map
R static/maps/utils/config.js.map
R static/maps/utils/deferred.js.map
R static/maps/utils/graph.js.map
R static/maps/utils/levenshtein.js.map
R static/maps/utils/localization.js.map
R static/maps/utils/metrics-logger.js.map
R static/maps/utils/natural-sort.js.map
R static/maps/utils/query-string-parsing.js.map
R static/maps/utils/uploadbox.js.map
R static/maps/utils/utils.js.map
R static/maps/viz/bbi-data-manager.js.map
R static/maps/viz/circster.js.map
R static/maps/viz/phyloviz.js.map
R static/maps/viz/sweepster.js.map
R static/maps/viz/trackster.js.map
R static/maps/viz/trackster/filters.js.map
R static/maps/viz/trackster/painters.js.map
R static/maps/viz/trackster/slotting.js.map
R static/maps/viz/trackster/tracks.js.map
R static/maps/viz/trackster/util.js.map
R static/maps/viz/visualization.js.map
R static/maps/viz/viz_views.js.map
M static/scripts/admin.toolshed.js
M static/scripts/bundled/admin.bundled.js
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A static/scripts/bundled/adminToolshed.bundled.js
M static/scripts/bundled/analysis.bundled.js
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A static/scripts/bundled/extended.bundled.js
A static/scripts/bundled/library.bundled.js
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R static/scripts/bundled/libs.bundled.js.map
M static/scripts/bundled/login.bundled.js
R static/scripts/bundled/login.bundled.js.map
A static/scripts/bundled/masthead.bundled.js
A static/scripts/bundled/viz.bundled.js
A static/scripts/bundled/workflow.bundled.js
M static/scripts/galaxy.interactive_environments.js
M static/scripts/galaxy.js
M static/scripts/galaxy.library.js
M static/scripts/galaxy.pages.js
M static/scripts/i18n.js
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M static/scripts/layout/panel.js
M static/scripts/layout/router.js
M static/scripts/layout/scratchbook.js
R static/scripts/libs/bibtex.js
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M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/base/controlled-fetch-collection.js
R static/scripts/mvc/citation/citation-model.js
R static/scripts/mvc/citation/citation-view.js
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-li-edit.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/dataset/states.js
M static/scripts/mvc/form/form-data.js
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M static/scripts/mvc/lazy/lazy-limited.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/library/library-util.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tool-genomespace.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-queue-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
M static/scripts/mvc/toolshed/repository-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/icon-button.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-select-ftp.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/collection/collection-row.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
M static/scripts/mvc/upload/default/default-row.js
M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
M static/scripts/mvc/upload/upload-extension.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view-node.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/de/locale.js
M static/scripts/nls/es/locale.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/onload.js
A static/scripts/packed
M static/scripts/polyfills.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/ui/editable-text.js
M static/scripts/ui/fa-icon-button.js
M static/scripts/ui/filter-control.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/ui/popupmenu.js
M static/scripts/ui/scroll-panel.js
M static/scripts/ui/search-input.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/async-save-text.js
M static/scripts/utils/config.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/levenshtein.js
M static/scripts/utils/localization.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/natural-sort.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
M static/style/blue/base.css
M static/style/blue/trackster.css
R templates/admin/library/grid.mako
R templates/admin/library/new_library.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
R templates/search/index.mako
M templates/show_params.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/base_panels.mako
R templates/webapps/galaxy/external_services/generic_jquery_grid.mako
R templates/webapps/galaxy/external_services/generic_json.mako
R templates/webapps/galaxy/external_services/json_common.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
R templates/webapps/galaxy/history/citations.mako
R templates/webapps/galaxy/library/common/browse_library.mako
R templates/webapps/galaxy/library/common/browse_library_opt.mako
R templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/library/common/folder_info.mako
R templates/webapps/galaxy/library/common/folder_permissions.mako
R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
R templates/webapps/galaxy/library/common/ldda_edit_info.mako
R templates/webapps/galaxy/library/common/ldda_info.mako
R templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_info.mako
R templates/webapps/galaxy/library/common/library_dataset_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_search_results.mako
R templates/webapps/galaxy/library/common/library_info.mako
R templates/webapps/galaxy/library/common/library_item_info.mako
R templates/webapps/galaxy/library/common/library_permissions.mako
R templates/webapps/galaxy/library/common/move_library_item.mako
R templates/webapps/galaxy/library/common/new_folder.mako
R templates/webapps/galaxy/library/common/upload.mako
R templates/webapps/galaxy/library/grid.mako
R templates/webapps/galaxy/library/index.mako
R templates/webapps/galaxy/user/list_users.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/run_stats.mako
M test-data/1.fastqsanger
M test-data/1.fastqsolexa
M test-data/simple_line_alternative.txt
M test-data/simple_lines_interleaved.txt
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_configuration.py
M test/api/test_dataset_collections.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_webhooks.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/populators.py
M test/base/testcase.py
M test/functional/test_toolbox.py
M test/functional/tools/bibtex.xml
A test/functional/tools/cat_data_and_sleep.xml
M test/functional/tools/collection_creates_dynamic_nested.xml
M test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/config_vars.xml
M test/functional/tools/create_2.xml
A test/functional/tools/for_workflows/count_list.xml
A test/functional/tools/for_workflows/count_multi_file.xml
A test/functional/tools/for_workflows/empty_list.xml
A test/functional/tools/identifier_in_actions.xml
A test/functional/tools/output_filter_with_input.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/twilltestcase.py
A test/functional/webhooks/tour_generator
M test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/driver_factory.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_local_job_cancellation.py
R test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_mules_as_job_handlers.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/test_workflow_scheduling_options.py
M test/manual/workflows_scaling.py
R test/qunit/Gruntfile.js
R test/qunit/README.txt
R test/qunit/package.json
R test/qunit/scripts
R test/qunit/test-app.js
R test/qunit/test-common.js
R test/qunit/test-data/bootstrapped.js
R test/qunit/test-data/fakeserver.js
R test/qunit/test-data/job-dag-1.js
R test/qunit/test-data/paired-collection-creator.data.js
R test/qunit/tests/form_tests.html
R test/qunit/tests/form_tests.js
R test/qunit/tests/galaxy-app-base.html
R test/qunit/tests/galaxy-app-base.js
R test/qunit/tests/graph.html
R test/qunit/tests/graph.js
R test/qunit/tests/hda-base.html
R test/qunit/tests/hda-base.js
R test/qunit/tests/history_contents_model_tests.html
R test/qunit/tests/history_contents_model_tests.js
R test/qunit/tests/job-dag.html
R test/qunit/tests/job-dag.js
R test/qunit/tests/list-of-pairs-collection-creator.html
R test/qunit/tests/list-of-pairs-collection-creator.js
R test/qunit/tests/masthead_tests.html
R test/qunit/tests/masthead_tests.js
R test/qunit/tests/metrics-logger.html
R test/qunit/tests/metrics-logger.js
R test/qunit/tests/modal_tests.html
R test/qunit/tests/modal_tests.js
R test/qunit/tests/page_tests.html
R test/qunit/tests/page_tests.js
R test/qunit/tests/popover_tests.html
R test/qunit/tests/popover_tests.js
R test/qunit/tests/ui_tests.html
R test/qunit/tests/ui_tests.js
R test/qunit/tests/upload_dialog_tests.html
R test/qunit/tests/upload_dialog_tests.js
R test/qunit/tests/utils_test.html
R test/qunit/tests/utils_test.js
R test/qunit/tests/workflow_editor_tests.html
R test/qunit/tests/workflow_editor_tests.js
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
A test/selenium_tests/test_history_copy_elements.py
M test/selenium_tests/test_history_dataset_state.py
A test/selenium_tests/test_history_multi_view.py
A test/selenium_tests/test_history_panel_collections.py
A test/selenium_tests/test_history_panel_pagination.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_contents.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_stock_tours.py
A test/selenium_tests/test_tool_describing_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample
M test/unit/config/1607_root_filters/config/galaxy.ini
M test/unit/config/1607_root_samples/config/galaxy.ini
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_objectstore.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_conda_resolution.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
A test/unit/tools/test_tool_validation.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_watcher.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M tools/data_source/data_source.py
M tools/data_source/microbial_import.xml
M tools/data_source/upload.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/phenotype_association/senatag.py
M tools/stats/gsummary.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into beta_tool_install_fixes and repack.
Commit: 3a9d63c69005602d32212208c69729bc4813ad5e
https://github.com/galaxyproject/galaxy/commit/3a9d63c69005602d32212208c697…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M static/scripts/bundled/extended.bundled.js
M static/scripts/mvc/toolshed/repository-view.js
Log Message:
-----------
Merge pull request #4944 from mvdbeek/beta_tool_install_fixes
Fix revision selection during (beta) repository installation
Compare: https://github.com/galaxyproject/galaxy/compare/c0b1337f26b4...3a9d63c69005
1
0
[galaxyproject/galaxy] 143a2d: Implement Multilingualization support on workflow ...
by GitHub 07 Dec '17
by GitHub 07 Dec '17
07 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 143a2db7adf05ba8e34d145327c0aaa467e1a460
https://github.com/galaxyproject/galaxy/commit/143a2db7adf05ba8e34d145327c0…
Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com>
Date: 2017-11-27 (Mon, 27 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/ja/locale.js
Log Message:
-----------
Implement Multilingualization support on workflow page
Commit: 81bf05494bc0a29ff0bcb6b1ebe741e910ff1886
https://github.com/galaxyproject/galaxy/commit/81bf05494bc0a29ff0bcb6b1ebe7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M .gitignore
M Makefile
M client/README.md
R client/galaxy/scripts/apps/admin-toolshed.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/extended.js
R client/galaxy/scripts/apps/library.js
R client/galaxy/scripts/apps/masthead.js
R client/galaxy/scripts/apps/viz.js
R client/galaxy/scripts/apps/workflow.js
A client/galaxy/scripts/components/Citations.vue
A client/galaxy/scripts/components/HistoryImport.vue
A client/galaxy/scripts/components/UserAPIKeys.vue
R client/galaxy/scripts/components/citations.vue
R client/galaxy/scripts/components/user_api_keys.vue
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
A 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-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.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-portlet.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/visualization/visualization-model.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/qunit/test.js
M client/galaxy/scripts/qunit/tests/form_tests.js
R client/galaxy/scripts/qunit/tests/galaxy-app-base.js
A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js
R client/galaxy/scripts/qunit/tests/graph.js
A client/galaxy/scripts/qunit/tests/graph_tests.js
R client/galaxy/scripts/qunit/tests/hda-base.js
A client/galaxy/scripts/qunit/tests/hda_base_tests.js
M client/galaxy/scripts/qunit/tests/history_contents_model_tests.js
R client/galaxy/scripts/qunit/tests/job-dag.js
A client/galaxy/scripts/qunit/tests/job_dag_tests.js
R client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js
A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
R client/galaxy/scripts/qunit/tests/metrics-logger.js
A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js
M client/galaxy/scripts/qunit/tests/modal_tests.js
M client/galaxy/scripts/qunit/tests/page_tests.js
M client/galaxy/scripts/qunit/tests/popover_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/qunit/tests/upload_dialog_tests.js
R client/galaxy/scripts/qunit/tests/utils_test.js
A client/galaxy/scripts/qunit/tests/utils_tests.js
M client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/list-item.less
M client/galaxy/style/less/ui.less
M client/gulpfile.js
M client/karma.config.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/error_report.yml.sample
R config/external_service_types_conf.xml.sample
M config/galaxy.ini.sample
M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample
M config/plugins/visualizations/charts/static/client/app.js
M config/plugins/visualizations/charts/static/client/components/model.js
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/client/views/description.js
M config/plugins/visualizations/charts/static/client/views/editor.js
M config/plugins/visualizations/charts/static/client/views/groups.js
M config/plugins/visualizations/charts/static/client/views/settings.js
M config/plugins/visualizations/charts/static/client/views/viewer.js
M config/plugins/visualizations/charts/static/client/views/viewport.js
M config/plugins/visualizations/charts/webpack.config.js
R config/plugins/visualizations/scatterplot/Gruntfile.js
R config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js
R config/plugins/visualizations/scatterplot/src/scatterplot-display.js
R config/plugins/visualizations/scatterplot/src/scatterplot-model.js
M config/plugins/visualizations/scatterplot/src/scatterplot.js
M config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
R config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
A config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js
M config/plugins/visualizations/scatterplot/static/worker-stats.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
A config/plugins/visualizations/scatterplot/webpack.config.js
M config/workflow_schedulers_conf.xml.sample
M cron/build_chrom_db.py
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
R external_service_types/454_life_sciences.xml
R external_service_types/applied_biosystems_solid.xml
R external_service_types/pacific_biosciences_smrt_portal.xml
R external_service_types/simple_unknown_sequencer.xml
M lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/structure.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
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.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/454Score.pdf
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
R lib/galaxy/external_services/__init__.py
R lib/galaxy/external_services/actions.py
R lib/galaxy/external_services/parameters.py
R lib/galaxy/external_services/result_handlers/__init__.py
R lib/galaxy/external_services/result_handlers/basic.py
R lib/galaxy/external_services/service.py
M lib/galaxy/jobs/__init__.py
R lib/galaxy/jobs/deferred/__init__.py
R lib/galaxy/jobs/deferred/data_transfer.py
R lib/galaxy/jobs/deferred/manual_data_transfer.py
R lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/jobs.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/model/tool_shed_install/__init__.py
R lib/galaxy/sample_tracking/__init__.py
R lib/galaxy/sample_tracking/data_transfer.py
R lib/galaxy/sample_tracking/external_service_types.py
R lib/galaxy/sample_tracking/request_types.py
R lib/galaxy/sample_tracking/sample.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/imp_history_from_archive.xml
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/parser/output_objects.py
A lib/galaxy/tools/repositories.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/compression_utils.py
A lib/galaxy/util/facts.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/image_util.py
R lib/galaxy/util/multi_byte.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/properties.py
A lib/galaxy/util/renamed_temporary_file.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
A lib/galaxy/web/stack/message.py
A lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
R manage_tools.sh
M run.sh
M run_reports.sh
M run_tool_shed.sh
M scripts/api/data_manager_example_execute.py
M scripts/api/display.py
M scripts/common_startup_functions.sh
M scripts/db_shell.py
M scripts/galaxy-main
A scripts/get_uwsgi_args.py
R scripts/manage_tools.py
M scripts/microbes/harvest_bacteria.py
R static/GruntFile.js.map
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/adminToolshed.bundled.js
M static/scripts/bundled/analysis.bundled.js
A static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/library.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
M static/scripts/bundled/masthead.bundled.js
M static/scripts/bundled/viz.bundled.js
M static/scripts/bundled/workflow.bundled.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
A static/scripts/mvc/history/job-states-model.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/workflow/workflow-canvas.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/packed
M static/scripts/utils/utils.js
M static/scripts/viz/trackster.js
M static/style/blue/base.css
M templates/webapps/galaxy/base_panels.mako
R templates/webapps/galaxy/external_services/generic_jquery_grid.mako
R templates/webapps/galaxy/external_services/generic_json.mako
R templates/webapps/galaxy/external_services/json_common.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/workflow/editor.mako
M test-data/1.fastqsanger
M test-data/1.fastqsolexa
M test-data/simple_line_alternative.txt
M test-data/simple_lines_interleaved.txt
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_pages.py
M test/api/test_tools.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_webhooks.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/populators.py
M test/functional/test_toolbox.py
M test/functional/tools/bibtex.xml
M test/functional/tools/collection_creates_dynamic_nested.xml
M test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/config_vars.xml
A test/functional/tools/for_workflows/count_list.xml
A test/functional/tools/for_workflows/count_multi_file.xml
A test/functional/tools/for_workflows/empty_list.xml
A test/functional/tools/identifier_in_actions.xml
A test/functional/tools/output_filter_with_input.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
M test/integration/test_local_job_cancellation.py
R test/integration/test_maximum_worklfow_invocation_duration.py
A test/integration/test_mules_as_job_handlers.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/test_workflow_scheduling_options.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
A test/selenium_tests/test_history_copy_elements.py
A test/selenium_tests/test_history_multi_view.py
A test/selenium_tests/test_history_panel_collections.py
A test/selenium_tests/test_history_panel_pagination.py
M test/selenium_tests/test_tool_form.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional_tests.py
A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample
M test/unit/dataset_collections/test_matching.py
M test/unit/jobs/test_job_configuration.py
A test/unit/tools/test_tool_validation.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/workflows/test_workflow_progress.py
M tools/data_source/data_source.py
M tools/data_source/upload.py
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/dev' into workflow_page_translation
Commit: e93821152432081dcfa08b1550e6c4d11e22abf7
https://github.com/galaxyproject/galaxy/commit/e93821152432081dcfa08b1550e6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/ja/locale.js
Log Message:
-----------
Repack to merge PR.
Commit: c0b1337f26b4072dca8cdf0144a28799b524d3c0
https://github.com/galaxyproject/galaxy/commit/c0b1337f26b4072dca8cdf0144a2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/ja/locale.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/ja/locale.js
Log Message:
-----------
Merge pull request #5077 from manabuishii/workflow_page_translation
Implement Multilingualization support on workflow page
Compare: https://github.com/galaxyproject/galaxy/compare/30e2736cc4fc...c0b1337f26b4
1
0
[galaxyproject/galaxy] f7820e: Do not write shed_tool_data_table_config in place
by GitHub 07 Dec '17
by GitHub 07 Dec '17
07 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: f7820e82380f7ea69ba56037a3f463352ef36807
https://github.com/galaxyproject/galaxy/commit/f7820e82380f7ea69ba56037a3f4…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/galaxy/tools/data/__init__.py
A lib/galaxy/util/renamed_temporary_file.py
Log Message:
-----------
Do not write shed_tool_data_table_config in place
This should prevent errors such as:
```
galaxy.util ERROR 2017-11-17 09:20:12,842 Error parsing file /data/users/mvandenb/gx/config/shed_tool_data_table_conf.xml
Traceback (most recent call last):
File "lib/galaxy/util/__init__.py", line 217, in parse_xml
root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget()))
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 657, in parse
self._root = parser.close()
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1654, in close
self._raiseerror(v)
File "/usr/lib/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
raise err
ParseError: no element found: line 1, column 0
```
reported in https://github.com/galaxyproject/galaxy/issues/5031.
Commit: a2b8e445d85b50265da52c06f017c9c78be953b6
https://github.com/galaxyproject/galaxy/commit/a2b8e445d85b50265da52c06f017…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/galaxy/model/tool_shed_install/__init__.py
Log Message:
-----------
Fix installation of data manager revision updates
Without this updates of data managers fails with
```
AttributeError: 'NoneType' object has no attribute 'get'
File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__
iterable = self.application(environ, start_response)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__
return self.application(environ, start_response)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__
return self.application(environ, start_response)
File "galaxy/web/framework/base.py", line 136, in __call__
return self.handle_request(environ, start_response)
File "galaxy/web/framework/base.py", line 215, in handle_request
body = method(trans, **kwargs)
File "galaxy/web/framework/decorators.py", line 98, in decorator
return func(self, trans, *args, **kwargs)
File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 1849, in update_to_changeset_revision
persist=True)
File "tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py", line 30, in __init__
metadata_dict=metadata_dict, user=None)
File "tool_shed/metadata/metadata_generator.py", line 63, in __init__
self.metadata_dict = {'shed_config_filename': self.shed_config_dict.get('config_filename', None)}
```
Commit: d44a20cef098abf905f8525c42eb7f37d39f4ad9
https://github.com/galaxyproject/galaxy/commit/d44a20cef098abf905f8525c42eb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/metadata/metadata_generator.py
Log Message:
-----------
Use a temporary ToolDataTableManager when generating metadata
Otherwise loaded data tables bleed into the app-wide data tables. This can be
seen with lots of data tables pointing to (non-existing, at that point)
temporary files after a metadata reset in the galaxy admin panel,
but it can also cause failure to install tools with entirely new data tables.
Commit: 561f71ec50ee6708913d57955456faa1932c4cac
https://github.com/galaxyproject/galaxy/commit/561f71ec50ee6708913d57955456…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/tool_shed/tools/data_table_manager.py
Log Message:
-----------
Avoid manipulating global toll data tables
Commit: c02d9363c45b7272f8b507f6c46aecf867faee5d
https://github.com/galaxyproject/galaxy/commit/c02d9363c45b7272f8b507f6c46a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Fix copying of loc.sample files
`filename` should be joined with the tool_path, as evidenced by other uses of
copy_sample_file.
Commit: fe6033fb22a23d4004a70de101e3f9597d0c6912
https://github.com/galaxyproject/galaxy/commit/fe6033fb22a23d4004a70de101e3…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/tools/tool_validator.py
Log Message:
-----------
Avoid global changes to app.config.tool_data_path
Commit: 7df9dce63d635d66a0a9ce5045135ab49b7ef506
https://github.com/galaxyproject/galaxy/commit/7df9dce63d635d66a0a9ce504513…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
Log Message:
-----------
Rename the ToolDataTableManager that deals with repository data to ShedToolDataTableManager to avoid confusion
Commit: b03f16ed49074ef98ba7ecd7ed9f70123e196ace
https://github.com/galaxyproject/galaxy/commit/b03f16ed49074ef98ba7ecd7ed9f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/tools/tool_validator.py
Log Message:
-----------
Load tools directly from source and avoid loading via toolbox
Commit: c0887d72f8d37ee7c608fa0e41d2455956e6791a
https://github.com/galaxyproject/galaxy/commit/c0887d72f8d37ee7c608fa0e41d2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
Log Message:
-----------
Fix missing index file check
Commit: 55e458262b4184557842312c77f70dc1f5f3903c
https://github.com/galaxyproject/galaxy/commit/55e458262b4184557842312c77f7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
A lib/galaxy/util/miniapp.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
Log Message:
-----------
Add miniapp to avoid manipulating global settings
Commit: ab21f303af8d53fe543974ed48e7d0614db2de22
https://github.com/galaxyproject/galaxy/commit/ab21f303af8d53fe543974ed48e7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/galaxy/util/miniapp.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Always use MiniApp when using ToolValidator
Commit: f08f4733050922c4177d84ec6f2550dd53cc8fcb
https://github.com/galaxyproject/galaxy/commit/f08f4733050922c4177d84ec6f25…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Only parse citations if app has citations_manager
Commit: d3261096c831a8539aeeae5ccf4e6734593f91a1
https://github.com/galaxyproject/galaxy/commit/d3261096c831a8539aeeae5ccf4e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/galaxy/util/miniapp.py
M lib/tool_shed/tools/tool_validator.py
Log Message:
-----------
Fix linting issues and fix data manager installation
Commit: c1630c244fc4700998e0d23130f7120344b303b2
https://github.com/galaxyproject/galaxy/commit/c1630c244fc4700998e0d23130f7…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
A lib/galaxy/tools/repositories/validationcontext.py
R lib/galaxy/util/miniapp.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Move and rename MiniApp to ValidationContext
This better describes what it used for and since it is tool specific, fits
better here that in utils. Thanks @jmchilton for the suggestion.
Commit: 93442f621bea51bd242f2b67e7d201bc409f9fe9
https://github.com/galaxyproject/galaxy/commit/93442f621bea51bd242f2b67e7d2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
A lib/galaxy/tools/repositories.py
R lib/galaxy/tools/repositories/validationcontext.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/util/workflow_util.py
Log Message:
-----------
Move ValidationContext to right path
Commit: 482c9cce76c56bee840a87f25b0a17b8937444f5
https://github.com/galaxyproject/galaxy/commit/482c9cce76c56bee840a87f25b0a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/tool_shed/tools/tool_validator.py
Log Message:
-----------
Remove more unused variables
Commit: db88175b9fffe76cfd9013a6e6d6cfb9c573c354
https://github.com/galaxyproject/galaxy/commit/db88175b9fffe76cfd9013a6e6d6…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
Log Message:
-----------
Use ValidationContext data tables instead of separately passing in relevant data tables
Commit: fd4737d0ecade2dd3f13d51756f90899920ef2a4
https://github.com/galaxyproject/galaxy/commit/fd4737d0ecade2dd3f13d51756f9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/util/tool_util.py
Log Message:
-----------
Don't reload tools, new indexes and data tables are recognized without a reload
Commit: f97774be82108d94fecc29dcf98f1fe833a4ece0
https://github.com/galaxyproject/galaxy/commit/f97774be82108d94fecc29dcf98f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/galaxy/tools/repositories.py
Log Message:
-----------
Change ValidationContext.build_file_path to be file
Also simplify cleanup code.
Commit: 1b48ff3dd15ebde13382afdb41cfb200a3c883cc
https://github.com/galaxyproject/galaxy/commit/1b48ff3dd15ebde13382afdb41cf…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/galaxy/tools/parameters/basic.py
Log Message:
-----------
Skip format parsing if datatypes registry contains no datatypes
Commit: 78e1478c7f9c6f3c232c6c91263c7bb28dec5c88
https://github.com/galaxyproject/galaxy/commit/78e1478c7f9c6f3c232c6c91263c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/tool_shed/metadata/repository_metadata_manager.py
Log Message:
-----------
Remove unnecessary tool data table resets
Commit: e65a2490c108929043a685eeca6bb89b6ade0b9c
https://github.com/galaxyproject/galaxy/commit/e65a2490c108929043a685eeca6b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/galaxy/tools/repositories.py
M lib/tool_shed/tools/data_table_manager.py
Log Message:
-----------
Linting fixes
Commit: 4f162f28041d6c0ee3b551d589339d4048b5b7e1
https://github.com/galaxyproject/galaxy/commit/4f162f28041d6c0ee3b551d58933…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-03 (Sun, 03 Dec 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample
A test/unit/tools/test_tool_validation.py
Log Message:
-----------
Add unit test for ValidationContext and ToolValidator
Commit: 30e2736cc4fc82cdf32437c60934a0e8e6bac453
https://github.com/galaxyproject/galaxy/commit/30e2736cc4fc82cdf32437c60934…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths:
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/parameters/basic.py
A lib/galaxy/tools/repositories.py
A lib/galaxy/util/renamed_temporary_file.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample
A test/unit/tools/test_tool_validation.py
Log Message:
-----------
Merge pull request #5119 from mvdbeek/dev_toolshed_install_improvements_2
Improve tool validation and metadata generation
Compare: https://github.com/galaxyproject/galaxy/compare/a901264ca745...30e2736cc4fc
1
0
[galaxyproject/galaxy] 4a7045: Merge remote-tracking branch 'origin/release_17.05...
by GitHub 06 Dec '17
by GitHub 06 Dec '17
06 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4a7045c8d2102d2e6188df222e5b128b8fbe7534
https://github.com/galaxyproject/galaxy/commit/4a7045c8d2102d2e6188df222e5b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-24 (Mon, 24 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.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/tours.js
M client/galaxy/style/less/ui.less
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/compression_utils.py
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tours.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tours.js
M static/style/blue/base.css
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/webhooks/trans_object/config/trans_object.yaml
Log Message:
-----------
Merge remote-tracking branch 'origin/release_17.05'
Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d
https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M config/datatypes_conf.xml.sample
M create_db.sh
M extract_dataset_parts.sh
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/deps/installable.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/workflow/modules.py
M manage_db.sh
M manage_tools.sh
M static/maps/mvc/base/controlled-fetch-collection.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/base/controlled-fetch-collection.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Merge branch 'release_17.05'
Commit: 15372f7369137b964534e9ddb8e81fb150dc2677
https://github.com/galaxyproject/galaxy/commit/15372f7369137b964534e9ddb8e8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-31 (Tue, 31 Oct 2017)
Changed paths:
A .ci/autopep8.sh
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/docker-compose.yml
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CITATION
M CONTRIBUTING.md
M Makefile
M README.rst
A SECURITY_POLICY.md
M client/bower.json
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
R client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/apps/panels/history-panel.js
A client/galaxy/scripts/apps/panels/tool-panel.js
R client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.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/dataset/data.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-view.js
A client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-model.js
A 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
A client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/options-menu.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
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
A client/galaxy/scripts/mvc/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/tool/tools.js
A client/galaxy/scripts/mvc/toolshed/categories-view.js
A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repo-status-view.js
A client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repository-view.js
A client/galaxy/scripts/mvc/toolshed/shed-list-view.js
A client/galaxy/scripts/mvc/toolshed/toolshed-model.js
A client/galaxy/scripts/mvc/toolshed/util.js
A client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.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-list.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/upload/upload-ftp.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/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
A client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
A client/galaxy/scripts/mvc/workflow/workflow.js
A client/galaxy/scripts/nls/de/locale.js
A client/galaxy/scripts/nls/es/locale.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/galaxy_variables.less
M client/galaxy/style/less/history.less
R client/galaxy/style/less/iphone.less
M client/galaxy/style/less/library.less
A client/galaxy/style/less/theme/plain.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/style.js
A client/package-lock.json
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M client/toolshed/scripts/mvc/groups/group-model.js
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
A config/error_report.yml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/lmod_modules_mapping.yml.sample
M config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/config/neo.xml
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
M config/plugins/tours/core.history.yaml
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
A config/plugins/visualizations/unipept/README.md
A config/plugins/visualizations/unipept/config/unipept.xml
A config/plugins/visualizations/unipept/static/style.css
A config/plugins/visualizations/unipept/static/tooltip.css
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map
A config/plugins/visualizations/unipept/static/unipept_viz.js
A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png
A config/plugins/visualizations/unipept/templates/unipept.mako
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M lib/galaxy/config.py
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M lib/galaxy/webapps/galaxy/controllers/library_common.py
R lib/galaxy/webapps/galaxy/controllers/mobile.py
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M lib/galaxy/webapps/galaxy/controllers/requests.py
M lib/galaxy/webapps/galaxy/controllers/requests_admin.py
M lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
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M lib/galaxy/webapps/reports/buildapp.py
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M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/tools.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
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M lib/galaxy/webapps/tool_shed/api/categories.py
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M lib/galaxy/webapps/tool_shed/api/groups.py
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M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/galaxy.js
M static/scripts/galaxy.library.js
M static/scripts/galaxy.pages.js
M static/scripts/layout/menu.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
A static/scripts/layout/router.js
M static/scripts/layout/scratchbook.js
M static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/dataset/data.js
A static/scripts/mvc/dataset/dataset-edit-attributes.js
A static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-view.js
A static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/grid/grid-model.js
A static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
A static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
A static/scripts/mvc/tool/tool-genomespace.js
M static/scripts/mvc/tool/tools.js
A static/scripts/mvc/toolshed/categories-view.js
A static/scripts/mvc/toolshed/repo-queue-view.js
A static/scripts/mvc/toolshed/repo-status-view.js
A static/scripts/mvc/toolshed/repositories-view.js
A static/scripts/mvc/toolshed/repository-queue-view.js
A static/scripts/mvc/toolshed/repository-view.js
A static/scripts/mvc/toolshed/shed-category-view.js
A static/scripts/mvc/toolshed/shed-list-view.js
A static/scripts/mvc/toolshed/shed-repo-details-view.js
A static/scripts/mvc/toolshed/shed-repo-list-view.js
A static/scripts/mvc/toolshed/sheds-list-view.js
A static/scripts/mvc/toolshed/toolshed-model.js
A static/scripts/mvc/toolshed/util.js
A static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
A static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-view.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/webhooks.js
A static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-manager.js
A static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
A static/scripts/mvc/workflow/workflow.js
A static/scripts/nls/de/locale.js
A static/scripts/nls/es/locale.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/onload.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/scroll-panel.js
M static/scripts/utils/graph.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/visualization.js
M static/style/blue/base.css
R static/style/blue/iphone.css
M static/style/blue/library.css
M static/toolshed/maps/mvc/groups/group-detail-view.js.map
M static/toolshed/maps/mvc/groups/group-list-view.js.map
M static/toolshed/maps/mvc/groups/group-listrow-view.js.map
M static/toolshed/maps/mvc/groups/group-model.js.map
M static/toolshed/scripts/mvc/groups/group-detail-view.js
M static/toolshed/scripts/mvc/groups/group-list-view.js
M static/toolshed/scripts/mvc/groups/group-listrow-view.js
M static/toolshed/scripts/mvc/groups/group-model.js
M static/welcome.html.sample
R templates/admin/dataset_security/group/grid.mako
R templates/admin/dataset_security/group/group.mako
R templates/admin/dataset_security/group/group_create.mako
R templates/admin/dataset_security/group/group_rename.mako
R templates/admin/dataset_security/role/grid.mako
R templates/admin/dataset_security/role/role.mako
R templates/admin/dataset_security/role/role_create.mako
R templates/admin/dataset_security/role/role_rename.mako
R templates/admin/quota/grid.mako
R templates/admin/quota/quota.mako
R templates/admin/quota/quota_create.mako
R templates/admin/quota/quota_edit.mako
R templates/admin/quota/quota_rename.mako
R templates/admin/quota/quota_set_default.mako
R templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/grid.mako
R templates/admin/tool_version/grid.mako
R templates/admin/user/grid.mako
R templates/admin/user/reset_password.mako
R templates/admin/user/user.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/display_common.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/js-app.mako
M templates/sharing_base.mako
M templates/show_params.mako
M templates/tagging_common.mako
M templates/user/login.mako
M templates/user/logout.mako
M templates/user/register.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/admin/index.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
M templates/webapps/galaxy/base_panels.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/dataset/display.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
R templates/webapps/galaxy/dataset/errors.mako
R templates/webapps/galaxy/dataset/grid.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/grid.mako
R templates/webapps/galaxy/history/grid_js.mako
R templates/webapps/galaxy/history/list_published.mako
R templates/webapps/galaxy/history/shared_grid.mako
R templates/webapps/galaxy/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
R templates/webapps/galaxy/mobile/history/detail.mako
R templates/webapps/galaxy/mobile/history/list.mako
R templates/webapps/galaxy/mobile/index.mako
R templates/webapps/galaxy/mobile/manage_library.mako
R templates/webapps/galaxy/mobile/settings.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/page/index.mako
R templates/webapps/galaxy/page/list_published.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/visualization/list.mako
R templates/webapps/galaxy/visualization/list_published.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
R templates/webapps/galaxy/workflow/configure_menu.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/list_for_run.mako
R templates/webapps/galaxy/workflow/list_published.mako
R templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/tool_shed/admin/center.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
R templates/webapps/tool_shed/repository/grid.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/1.sam.gz
A test-data/5_Ig-like.gff
A test-data/bad.html.gz
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
A test-data/random-file
A test-data/test.vcf.gz
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_framework.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_search.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_tours.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/api_util.py
M test/base/driver_util.py
M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/populators.py
R test/base/test_db_util.py
A test/base/testcase.py
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R test/functional/database_contexts.py
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R test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/code_file.py
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
A test/functional/tools/identifier_source.xml
M test/functional/tools/metadata.xml
A test/functional/tools/mulled_example_multi_versionless.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
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M test/functional/tools/tool_provided_metadata_3.xml
A test/functional/tools/tool_provided_metadata_4.xml
A test/functional/tools/tool_provided_metadata_5.xml
A test/functional/tools/tool_provided_metadata_6.xml
A test/functional/tools/tool_provided_metadata_7.xml
A test/functional/tools/tool_provided_metadata_8.xml
A test/functional/tools/tool_provided_metadata_9.xml
A test/functional/tools/vcf_bgzip.xml
A test/functional/twilltestcase.py
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/functional/webhooks/trans_object/helper/__init__.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_config_options_users.py
A test/integration/test_data_manager_table_reload.py
M test/integration/test_maximum_worklfow_invocation_duration.py
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A test/integration/test_upload_configuration_options.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/tool_sheds_conf.xml
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M test/qunit/tests/ui_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_custom_builds.py
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M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
A test/selenium_tests/test_published_histories_grid.py
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A test/selenium_tests/test_saved_histories.py
A test/selenium_tests/test_sizzle_loading.py
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M test/shed_functional/functional/test_0060_workflows.py
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A test/unit/jobs/conditional_runners_job_conf.xml
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M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_panel.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/joiner.xml
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/wc_gnu.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
R tools/genomespace/genomespace_file_browser_dev.xml
R tools/genomespace/genomespace_file_browser_prod.xml
R tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
A tools/genomespace/genomespace_push.xml
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg.xml
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'release_17.09'
Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd
https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-05 (Tue, 05 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Migrate documentation for setting up a production instance to Galaxy.
This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).
This content currently includes:
- the production configuration page
- the cluster configuration page
- the job configuration page
- the scaling information page
- the ftp configuration page
- the top-level nginx page (for external auth content still linking out to the hub)
- the top-level apache page (for external auth content still linking out to the hub)
- the job metrics configuration page
Includes small tweaks to sphinx documentation generation.
- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs.
- Use AutoStructify for better Markdown integration.
Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:
- Update the job configuration page with information about XML macros.
- Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore).
- Updated list of dynamic job runner configuration parameters.
- Mention the ``raw`` attribute for ``env`` directives in the job configuration page.
- Mention the ``total_walltime`` limit added in #3217.
- Drop mentions of older URL-based job conf configuration stuff.
- Mention newer Local and Paramiko based shell runners in CLI section.
- Mention newer slurm job styles in CLI section.
- Improved Pulsar links.
- Fix dataset security link in Apache display sites config.
- Update job metrics page to link to a new Github issue instead of old Trello issues.
Commit: befa077cc444115e0cac738c2bd3ee786f7425d2
https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M doc/source/admin/jobs.md
Log Message:
-----------
Rework headings in jobs docs.
Thanks to comment from @erasche review.
Commit: b0c03240fd96ace2b25680e753fed0237264ec98
https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fe…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Merge pull request #5135 from jmchilton/17.09_admin_docs
[17.09] Migrate documentation for setting up a production instance to Galaxy.
Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43
https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba835…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Log Message:
-----------
Merge pull request #5141 from jmchilton/master
[17.09] Re-merge master into release_17.09.
Commit: a901264ca74594f358b4d95862cb0ccd29346fcf
https://github.com/galaxyproject/galaxy/commit/a901264ca74594f358b4d95862cb…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/4d30b4f9cc5c...a901264ca745
1
0
06 Dec '17
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: b7e05a012cb8dd3bf90f31f5c5a7df44587e97c0
https://github.com/galaxyproject/galaxy/commit/b7e05a012cb8dd3bf90f31f5c5a7…
Author: Ignacio Eguinoa <igegu(a)psb.ugent.be>
Date: 2017-11-01 (Wed, 01 Nov 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
otherwise it will overwrite linking source file
Commit: 19e5478cb8ffbd9d97db663bb1d04e52bed721a0
https://github.com/galaxyproject/galaxy/commit/19e5478cb8ffbd9d97db663bb1d0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-02 (Thu, 02 Nov 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #4911 from jmchilton/backport_4858
[17.09] Backport #4858
Commit: e3be7c31d59b69571bcee04599bdac6693426b89
https://github.com/galaxyproject/galaxy/commit/e3be7c31d59b69571bcee04599bd…
Author: Wolfgang Maier <wolfgang.maier(a)biologie.uni-freiburg.de>
Date: 2017-11-03 (Fri, 03 Nov 2017)
Changed paths:
M doc/source/releases/17.09_announce.rst
Log Message:
-----------
fix broken link in 17.09 announcement
Commit: 222ece4eabb6d080c6b8a0e327f8cf617b8a194f
https://github.com/galaxyproject/galaxy/commit/222ece4eabb6d080c6b8a0e327f8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-03 (Fri, 03 Nov 2017)
Changed paths:
M doc/source/releases/17.09_announce.rst
Log Message:
-----------
Merge pull request #4927 from wm75/patch-2
fix broken link in 17.09 announcement
Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3
https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Tolerate IOError in tool and data table watcher
Without these changes the watcher thread may die when manually deleting loc files:
```
Exception in thread Thread-7:
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run
self.dispatch_events(self.event_queue, self.timeout)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events
handler.dispatch(event)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch
self.on_any_event(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event
self._handle(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle
cur_hash = md5_hash_file(path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file
with open(path, 'rb') as afile:
IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc'
```
Similar problems could occur when deleting tool xml files.
Commit: 0207b0186ac7c3d61004718ff7b91c3ea0c52165
https://github.com/galaxyproject/galaxy/commit/0207b0186ac7c3d61004718ff7b9…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Specify TagAssociation class when copying a tag
This probably fixes https://github.com/galaxyproject/galaxy/issues/4975.
Otherwise if a collection is created from a HDA with a tag (i.e by splitting the dataset)
a HistoryDatasetAssociationTag would be added to a collection of
HistoryDatasetCollectionAssociationTags.
Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377
https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a007248…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-12 (Sun, 12 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Encode file content with utf-8
There shouldn't be any disadvantages over doing this only for specific elements.
This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378.
I have tested this with unicode strings in the name and info fields.
Commit: b978acbe62053596e5c2ae736c848a62dc936591
https://github.com/galaxyproject/galaxy/commit/b978acbe62053596e5c2ae736c84…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-12 (Sun, 12 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Revert "Remove downloading workflows through controller"
This reverts commit 1a4effa70e9ad8088e19ae334753b7a898d286aa.
This is used when downloading workflows with the save icom from "pages".
Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3
https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Open files in text-mode (thx @nsoranzo)
Commit: 6915007f85482648999768eecb9920da57b42e59
https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge pull request #4981 from mvdbeek/watcher_error_delete
[17.05][BUG] Tolerate IOError in tool and data table watcher
Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759
https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Merge pull request #4987 from mvdbeek/history_import_bug
[17.09][Bug] Encode file content with utf-8
Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0
https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc9800…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Commit: 3b523260551d15241de5dce3d1023790dcfd2250
https://github.com/galaxyproject/galaxy/commit/3b523260551d15241de5dce3d102…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #4988 from jmchilton/revert_export_to_file
[17.09] Revert export to file
Commit: e5587dcb64897e53900c05bde2afa32c945ce6a6
https://github.com/galaxyproject/galaxy/commit/e5587dcb64897e53900c05bde2af…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge pull request #4984 from mvdbeek/fix_crash_when_creating_collection_from_datasets_with_tags
[17.05][BUG] Specify TagAssociation class when copying a tag
Commit: 1a412bfb1b0497d9e3e2b8f9c348d7aa0f2478d6
https://github.com/galaxyproject/galaxy/commit/1a412bfb1b0497d9e3e2b8f9c348…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Commit: 06e9509d3868c885d41d94e455d7245f4af10156
https://github.com/galaxyproject/galaxy/commit/06e9509d3868c885d41d94e455d7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Allow get_history calls with create=False when evaluation workflows.
No reasons to prevent this I guess - since create means create if a history isn't available not force the creation of a history.
Commit: 0a6c2974204b3048456bc7ceba7793ab4774de9f
https://github.com/galaxyproject/galaxy/commit/0a6c2974204b3048456bc7ceba77…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Add missing ipaddress requirement
Broken in https://github.com/galaxyproject/galaxy/pull/4289 .
Fix https://github.com/galaxyproject/galaxy/issues/4999 .
Commit: 63f039b66fef6448f10ea639f2be5fb376cca05e
https://github.com/galaxyproject/galaxy/commit/63f039b66fef6448f10ea639f2be…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
remove the default override
since it is wrong and ignores the access permissions
Commit: 827ac9c0433f581166b5bd06b70a14a39f22ded2
https://github.com/galaxyproject/galaxy/commit/827ac9c0433f581166b5bd06b70a…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Do not attempt to visit parameters of invalid conditionals
Commit: 1457fa7f937522d4825bb814a927a87b2e363cc8
https://github.com/galaxyproject/galaxy/commit/1457fa7f937522d4825bb814a927…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Check for key/value errors only when testing conditional cases
Commit: 75f84bfc476ea94c22a38097d20f694265fcded6
https://github.com/galaxyproject/galaxy/commit/75f84bfc476ea94c22a38097d20f…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Add test cases to cover version changes
Commit: 9a13a4af7fe44f6482b075bba6cf3fc500226956
https://github.com/galaxyproject/galaxy/commit/9a13a4af7fe44f6482b075bba6cf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge pull request #5008 from martenson/fix-ldda-access-check
[16.07] history contents api - remove the default flag override
Commit: 4a2814227cd7509ee62a8f5a64190934b4169ae9
https://github.com/galaxyproject/galaxy/commit/4a2814227cd7509ee62a8f5a6419…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.07' into HEAD
Commit: 54b9b09fb2d232b53fa9430606040060d6b21a4e
https://github.com/galaxyproject/galaxy/commit/54b9b09fb2d232b53fa943060604…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_16.10' into HEAD
Commit: eab30c96522a5a558de4232320c87c1ef102d2d2
https://github.com/galaxyproject/galaxy/commit/eab30c96522a5a558de4232320c8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.01' into release_17.05
Commit: b25de8b003168ebced8fbc3bfce5274d32cc1ab7
https://github.com/galaxyproject/galaxy/commit/b25de8b003168ebced8fbc3bfce5…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_17.05' into HEAD
Commit: 9e9edb7e338bcf6a3d4174fc0d8e420a5184ad6b
https://github.com/galaxyproject/galaxy/commit/9e9edb7e338bcf6a3d4174fc0d8e…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-11-14 (Tue, 14 Nov 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Remove unnecessary name setting for non-group parameters
Commit: 64eced315887f19b7efd6334d4a28f91e8fd6116
https://github.com/galaxyproject/galaxy/commit/64eced315887f19b7efd6334d4a2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Fix comments
Commit: 18467e9b2cecb2102d17fd6734f1fb40c5321623
https://github.com/galaxyproject/galaxy/commit/18467e9b2cecb2102d17fd6734f1…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Merge pull request #5000 from nsoranzo/release_17.09_add_ipaddress_requirement
[17.09] Add missing ipaddress requirement
Commit: de1bd5f5d5af7b9e67180b115407fbc2ccb75a3e
https://github.com/galaxyproject/galaxy/commit/de1bd5f5d5af7b9e67180b115407…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/package-lock.json
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Fix workflow editor output attributes.
Commit: 5dc2254417667216dab982a4bc375a85d3b55316
https://github.com/galaxyproject/galaxy/commit/5dc2254417667216dab982a4bc37…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M lib/galaxy/work/context.py
Log Message:
-----------
Merge pull request #4997 from jmchilton/allow_create_false_in_work_context
[17.09] Allow get_history calls with create=False when evaluation workflows.
Commit: 2a0c7114dfafb0c91e3bafb03ae6ff4370ce9ed8
https://github.com/galaxyproject/galaxy/commit/2a0c7114dfafb0c91e3bafb03ae6…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/package-lock.json
M static/maps/mvc/workflow/workflow-forms.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/workflow/workflow-forms.js
Log Message:
-----------
Merge pull request #5022 from dannon/workflow_editor_fix_backport
[17.09] Fix workflow editor output attributes.
Commit: 1cfdf85879213018affc3ec19142e3ebccdb8c40
https://github.com/galaxyproject/galaxy/commit/1cfdf85879213018affc3ec19142…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
add ICM datatype for glimmer
Commit: f44175b03c1671e6db11f1b072c3cd704a95fd58
https://github.com/galaxyproject/galaxy/commit/f44175b03c1671e6db11f1b072c3…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
copy paste mistake...
Commit: f60a75c285830bff963bd31120f3420e9815dbe2
https://github.com/galaxyproject/galaxy/commit/f60a75c285830bff963bd31120f3…
Author: E Rasche <hxr(a)hx42.org>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/condor.py
Log Message:
-----------
extraneous %s
Commit: 59e9809585e2322382eaeb7b3e0270485b7e8db0
https://github.com/galaxyproject/galaxy/commit/59e9809585e2322382eaeb7b3e02…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/condor.py
Log Message:
-----------
Merge pull request #5048 from erasche/fix-ufr-6206
Remove extraneous %s in condor logging
Commit: a7c8edbaa448805e0211fc75e3888d8426e5fa38
https://github.com/galaxyproject/galaxy/commit/a7c8edbaa448805e0211fc75e388…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/wrappers.py
M test/api/test_tools.py
A test/functional/tools/identifier_in_actions.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Bug fix - expose proper element_identifier in tool action template expansions. (#5049)
xref https://github.com/galaxyproject/tools-iuc/commit/f57f1bf4816f212b83c08e0e3…
Commit: 0bb7612977a44422acdf9c7d559d555ece1d17da
https://github.com/galaxyproject/galaxy/commit/0bb7612977a44422acdf9c7d559d…
Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr>
Date: 2017-11-21 (Tue, 21 Nov 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
don't read too much
Commit: 8db4288ab5dcf379a669a5ae6ececc217b3c9da0
https://github.com/galaxyproject/galaxy/commit/8db4288ab5dcf379a669a5ae6ece…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Fixes galaxy startup when LC_TYPE=UTF-8 on os-x
Closes https://github.com/galaxyproject/galaxy/issues/2645.
Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f
https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031:
```
Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check
self.reload_callback()
File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda>
self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache)
File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox
_get_new_toolbox(app)
File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox
new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
File "lib/galaxy/tools/__init__.py", line 226, in __init__
app=app,
File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__
super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__
self._save_integrated_tool_panel()
File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel
self._write_integrated_tool_panel_config_file()
File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file
os.chmod(self._integrated_tool_panel_config, 0o644)
OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml'
```
Commit: adfb623224810a0f383dc4ddf88be4ce51d3aa71
https://github.com/galaxyproject/galaxy/commit/adfb623224810a0f383dc4ddf88b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
Fix metadata setting for Otu datatypes
I broke this in https://github.com/galaxyproject/galaxy/pull/4388.
I went through the other changes in that PR, and I believe this should be the
only error.
Figured out through the great detective work of @abernard.
Commit: a71d5aa2db41a289b9410b129e6e70652f456593
https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Merge pull request #5071 from mvdbeek/installation_fixes
[BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
Commit: f16491cd6506eb0734c415be1e0456faf9c1dd04
https://github.com/galaxyproject/galaxy/commit/f16491cd6506eb0734c415be1e04…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #5070 from mvdbeek/docutils_upgrade
[BUG][[17.09] Fixes galaxy startup when LC_TYPE=UTF-8 on os-x
Commit: a58586f0e4973aa6855142222ed8be124add9ad5
https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Cleanup SA objects between workflow invocation scheduling attempts.
This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more.
Commit: ed162d5a69a3fac061f6becf592e737eed678411
https://github.com/galaxyproject/galaxy/commit/ed162d5a69a3fac061f6becf592e…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-11-27 (Mon, 27 Nov 2017)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
Merge pull request #5072 from mvdbeek/metadata_investigation
[BUG][17.09] Fix metadata setting for Otu datatypes
Commit: 385aaf2bd7e2b1c79f4b21f0449aed98fc9d6446
https://github.com/galaxyproject/galaxy/commit/385aaf2bd7e2b1c79f4b21f0449a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-27 (Mon, 27 Nov 2017)
Changed paths:
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message:
-----------
Fix exception in admin panel
TypeError: Non-hexadecimal digit found
File "galaxy/web/framework/middleware/sentry.py", line 40, in __call__
iterable = self.application(environ, start_response)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__
return self.application(environ, start_response)
File "/bioinfo/guests/mvandenb/galaxy/.venv/local/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__
return self.application(environ, start_response)
File "galaxy/web/framework/base.py", line 136, in __call__
return self.handle_request(environ, start_response)
File "galaxy/web/framework/base.py", line 215, in handle_request
body = method(trans, **kwargs)
File "galaxy/web/framework/decorators.py", line 98, in decorator
return func(self, trans, *args, **kwargs)
File "galaxy/webapps/galaxy/controllers/admin_toolshed.py", line 660, in manage_repositories
return self.repository_installation_grid(trans, **kwd)
File "galaxy/web/framework/helpers/grids.py", line 85, in __call__
query = self.build_initial_query(trans, **kwargs)
File "tool_shed/galaxy_install/grids/admin_toolshed_grids.py", line 334, in build_initial_query
clause_list.append(self.model_class.table.c.id == trans.security.decode_id(tool_shed_repository_id))
File "galaxy/web/security/__init__.py", line 107, in decode_id
return int(id_cipher.decrypt(obj_id.decode('hex')).lstrip("!"))
File "encodings/hex_codec.py", line 42, in hex_decode
output = binascii.a2b_hex(input)
This is due to `tool_shed_repository_ids` being a json dump of a list
in certain consitions (noticed this after installing a new repository).
Commit: 0493763938ab6146dc383b735a7b3523914c2342
https://github.com/galaxyproject/galaxy/commit/0493763938ab6146dc383b735a7b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE
Commit: f6aedb0d2094256eb7f45ce7fc75f327db5b560c
https://github.com/galaxyproject/galaxy/commit/f6aedb0d2094256eb7f45ce7fc75…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Merge pull request #5042 from abretaud/icm_dt
[17.09] Add ICM datatype for glimmer
Commit: ff3a6b084931f532dbce9a6d82059cda0137e3e3
https://github.com/galaxyproject/galaxy/commit/ff3a6b084931f532dbce9a6d8205…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Merge pull request #5086 from mvdbeek/sentry_report_fix
[17.09] Always fill `message` to avoid KeyError for sentry ERROR_TEMPLATE
Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e
https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Merge pull request #5073 from jmchilton/backport_5045
[17.09] Backport #5045
Commit: e903cb708e2f33bccebf5a0dd89b3bfe13667e03
https://github.com/galaxyproject/galaxy/commit/e903cb708e2f33bccebf5a0dd89b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/tools/parameters/__init__.py
Log Message:
-----------
Merge pull request #5010 from guerler/fix_pages_workflows
[17.09] Do not visit child inputs of invalid conditionals
Commit: a82d325d18375797ce8ab53366320f3c9a772ab7
https://github.com/galaxyproject/galaxy/commit/a82d325d18375797ce8ab5336632…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
Log Message:
-----------
Merge pull request #5079 from mvdbeek/admin_panel_exception_fix
[17.09] Fix exception in admin panel
Commit: 72aa96c7bcc21d333c17dffa5a5623b8b5dc82e4
https://github.com/galaxyproject/galaxy/commit/72aa96c7bcc21d333c17dffa5a56…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/molecules.py
Log Message:
-----------
Stricter checks for SDF sniffing
I had a bunch of protein FASTA files being sniffed as 'sdf'.
Also fix https://github.com/galaxyproject/galaxy/issues/4558 .
Commit: 95579883de61fb50bf3b309c8ab871b41d0d10ac
https://github.com/galaxyproject/galaxy/commit/95579883de61fb50bf3b309c8ab8…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/test/chebi_57262.v3k.mol
A lib/galaxy/datatypes/test/github88.v3k.sdf
Log Message:
-----------
More precise SDF sniffer
First check 4th line: if this is conforming, scan up to 10000 lines.
Add 2 test files downloaded from:
https://github.com/rdkit/rdkit/tree/master/Code/GraphMol/FileParsers/test_d…
Commit: c41fc0a4275ad4640a086d9bdf4d6bf3aec8c197
https://github.com/galaxyproject/galaxy/commit/c41fc0a4275ad4640a086d9bdf4d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-02 (Sat, 02 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/molecules.py
A lib/galaxy/datatypes/test/chebi_57262.v3k.mol
A lib/galaxy/datatypes/test/github88.v3k.sdf
Log Message:
-----------
Merge pull request #5118 from mvdbeek/backport_sdf_sniffing_fixes
[17.09] Backport stricter checks for SDF sniffing #4729
Commit: d73bb6c6c6b4d7efad56ec46653d11e4542e8f9a
https://github.com/galaxyproject/galaxy/commit/d73bb6c6c6b4d7efad56ec46653d…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-12-04 (Mon, 04 Dec 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Fix ICM datatype sniffer config
Probably a bad merge in https://github.com/galaxyproject/galaxy/pull/5108
Commit: 22aa02f59496f9c10a855a3aac58f785a13124a2
https://github.com/galaxyproject/galaxy/commit/22aa02f59496f9c10a855a3aac58…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2017-12-04 (Mon, 04 Dec 2017)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
Merge pull request #5121 from mvdbeek/fix_icm_datatype_config
[17.09] Fix ICM datatype sniffer config
Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd
https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-05 (Tue, 05 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Migrate documentation for setting up a production instance to Galaxy.
This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).
This content currently includes:
- the production configuration page
- the cluster configuration page
- the job configuration page
- the scaling information page
- the ftp configuration page
- the top-level nginx page (for external auth content still linking out to the hub)
- the top-level apache page (for external auth content still linking out to the hub)
- the job metrics configuration page
Includes small tweaks to sphinx documentation generation.
- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs.
- Use AutoStructify for better Markdown integration.
Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:
- Update the job configuration page with information about XML macros.
- Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore).
- Updated list of dynamic job runner configuration parameters.
- Mention the ``raw`` attribute for ``env`` directives in the job configuration page.
- Mention the ``total_walltime`` limit added in #3217.
- Drop mentions of older URL-based job conf configuration stuff.
- Mention newer Local and Paramiko based shell runners in CLI section.
- Mention newer slurm job styles in CLI section.
- Improved Pulsar links.
- Fix dataset security link in Apache display sites config.
- Update job metrics page to link to a new Github issue instead of old Trello issues.
Commit: befa077cc444115e0cac738c2bd3ee786f7425d2
https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M doc/source/admin/jobs.md
Log Message:
-----------
Rework headings in jobs docs.
Thanks to comment from @erasche review.
Commit: b0c03240fd96ace2b25680e753fed0237264ec98
https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fe…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Merge pull request #5135 from jmchilton/17.09_admin_docs
[17.09] Migrate documentation for setting up a production instance to Galaxy.
Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43
https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba835…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Log Message:
-----------
Merge pull request #5141 from jmchilton/master
[17.09] Re-merge master into release_17.09.
Compare: https://github.com/galaxyproject/galaxy/compare/15372f736913...cd1454c40a43
1
0
[galaxyproject/galaxy] 4a7045: Merge remote-tracking branch 'origin/release_17.05...
by GitHub 06 Dec '17
by GitHub 06 Dec '17
06 Dec '17
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 4a7045c8d2102d2e6188df222e5b128b8fbe7534
https://github.com/galaxyproject/galaxy/commit/4a7045c8d2102d2e6188df222e5b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-07-24 (Mon, 24 Jul 2017)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hdca-li.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/tours.js
M client/galaxy/style/less/ui.less
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/tool_list/config/tool_list.yml
M lib/galaxy/datatypes/registry.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/compression_utils.py
M static/maps/mvc/dataset/dataset-li.js.map
M static/maps/mvc/form/form-input.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tours.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tours.js
M static/style/blue/base.css
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/webhooks/trans_object/config/trans_object.yaml
Log Message:
-----------
Merge remote-tracking branch 'origin/release_17.05'
Commit: 0a39bfcbf7dcd5d2801be4a6b36a4c34a2ff9b5d
https://github.com/galaxyproject/galaxy/commit/0a39bfcbf7dcd5d2801be4a6b36a…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-09-15 (Fri, 15 Sep 2017)
Changed paths:
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M config/datatypes_conf.xml.sample
M create_db.sh
M extract_dataset_parts.sh
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/tools/deps/installable.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/workflow/modules.py
M manage_db.sh
M manage_tools.sh
M static/maps/mvc/base/controlled-fetch-collection.js.map
A static/maps/mvc/job/job-params.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/base/controlled-fetch-collection.js
A static/scripts/mvc/job/job-params.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/ui/ui-select-content.js
Log Message:
-----------
Merge branch 'release_17.05'
Commit: 15372f7369137b964534e9ddb8e81fb150dc2677
https://github.com/galaxyproject/galaxy/commit/15372f7369137b964534e9ddb8e8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-10-31 (Tue, 31 Oct 2017)
Changed paths:
A .ci/autopep8.sh
M .ci/flake8_lint_include_list.txt
M .ci/jenkins/selenium/docker-compose.yml
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CITATION
M CONTRIBUTING.md
M Makefile
M README.rst
A SECURITY_POLICY.md
M client/bower.json
A client/galaxy/scripts/admin.toolshed.js
A client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
R client/galaxy/scripts/apps/history-panel.js
M client/galaxy/scripts/apps/login.js
A client/galaxy/scripts/apps/panels/admin-panel.js
A client/galaxy/scripts/apps/panels/history-panel.js
A client/galaxy/scripts/apps/panels/tool-panel.js
R client/galaxy/scripts/apps/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
A client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/jquery/jqtouch.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.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/dataset/data.js
A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
A client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-view.js
A client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-model.js
A 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
A client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/options-menu.js
A client/galaxy/scripts/mvc/job/job-params.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
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
A client/galaxy/scripts/mvc/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/tool/tools.js
A client/galaxy/scripts/mvc/toolshed/categories-view.js
A client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repo-status-view.js
A client/galaxy/scripts/mvc/toolshed/repositories-view.js
A client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
A client/galaxy/scripts/mvc/toolshed/repository-view.js
A client/galaxy/scripts/mvc/toolshed/shed-list-view.js
A client/galaxy/scripts/mvc/toolshed/toolshed-model.js
A client/galaxy/scripts/mvc/toolshed/util.js
A client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.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-list.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
A client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/upload/upload-ftp.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/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
A client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
A client/galaxy/scripts/mvc/workflow/workflow.js
A client/galaxy/scripts/nls/de/locale.js
A client/galaxy/scripts/nls/es/locale.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/galaxy_bootstrap/overrides.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/galaxy_variables.less
M client/galaxy/style/less/history.less
R client/galaxy/style/less/iphone.less
M client/galaxy/style/less/library.less
A client/galaxy/style/less/theme/plain.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/galaxy/style/source_material/circle.py
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/style.js
A client/package-lock.json
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M client/toolshed/scripts/mvc/groups/group-model.js
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/dependency_resolvers_conf.xml.sample
A config/error_report.yml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
A config/lmod_modules_mapping.yml.sample
M config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/config/allowed_images.yml.sample
M config/plugins/interactive_environments/neo/config/neo.ini.sample
M config/plugins/interactive_environments/neo/config/neo.xml
M config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
M config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
M config/plugins/tours/core.history.yaml
M config/plugins/visualizations/charts/static/client/components/screenshot.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
M config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
M config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
M config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
M config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
M config/plugins/visualizations/graphviz/static/js/toolPanelFunctions.js
A config/plugins/visualizations/unipept/README.md
A config/plugins/visualizations/unipept/config/unipept.xml
A config/plugins/visualizations/unipept/static/style.css
A config/plugins/visualizations/unipept/static/tooltip.css
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js
A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map
A config/plugins/visualizations/unipept/static/unipept_viz.js
A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png
A config/plugins/visualizations/unipept/templates/unipept.mako
M config/plugins/webhooks/demo/search/config/searchover.yaml
M config/plugins/webhooks/demo/search/static/script.js
M config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
A config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/static/script.js
A config/plugins/webhooks/demo/tour_generator/static/styles.css
R config/reports.ini.sample
A config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
R config/tool_shed.ini.sample
A config/tool_shed.yml.sample
A config/user_preferences_extra_conf.yml.sample
M contrib/galaxy.debian-init
M contrib/galaxy_supervisor.conf
M contrib/nagios/check_galaxy.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M cron/updateucsc.sh.sample
M doc/Makefile
R doc/patch.py
M doc/source/admin/authentication.md
M doc/source/admin/dependency_resolvers.rst
A doc/source/admin/reports.rst
A doc/source/admin/reports_options.rst
A doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/grt.rst
M doc/source/admin/special_topics/index.rst
M doc/source/admin/special_topics/mulled_containers.rst
R doc/source/api/api.rst
R doc/source/api/ts_api.rst
M doc/source/dev/build_a_job_runner.rst
A doc/source/dev/finding_and_improving_slow_code.rst
M doc/source/lib/galaxy.actions.rst
M doc/source/lib/galaxy.auth.providers.rst
M doc/source/lib/galaxy.auth.rst
A doc/source/lib/galaxy.containers.rst
M doc/source/lib/galaxy.dataset_collections.rst
M doc/source/lib/galaxy.dataset_collections.types.rst
M doc/source/lib/galaxy.datatypes.converters.rst
M doc/source/lib/galaxy.datatypes.dataproviders.rst
M doc/source/lib/galaxy.datatypes.display_applications.rst
M doc/source/lib/galaxy.datatypes.rst
M doc/source/lib/galaxy.datatypes.util.rst
M doc/source/lib/galaxy.dependencies.rst
M doc/source/lib/galaxy.eggs.rst
M doc/source/lib/galaxy.exceptions.rst
M doc/source/lib/galaxy.external_services.result_handlers.rst
M doc/source/lib/galaxy.external_services.rst
M doc/source/lib/galaxy.forms.rst
M doc/source/lib/galaxy.jobs.actions.rst
M doc/source/lib/galaxy.jobs.deferred.rst
M doc/source/lib/galaxy.jobs.metrics.collectl.rst
M doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
M doc/source/lib/galaxy.jobs.metrics.rst
M doc/source/lib/galaxy.jobs.rst
M doc/source/lib/galaxy.jobs.runners.rst
M doc/source/lib/galaxy.jobs.runners.state_handlers.rst
M doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
M doc/source/lib/galaxy.jobs.runners.util.cli.rst
M doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
M doc/source/lib/galaxy.jobs.runners.util.condor.rst
A doc/source/lib/galaxy.jobs.runners.util.drmaa.rst
M doc/source/lib/galaxy.jobs.runners.util.job_script.rst
M doc/source/lib/galaxy.jobs.runners.util.rst
M doc/source/lib/galaxy.jobs.splitters.rst
M doc/source/lib/galaxy.managers.rst
M doc/source/lib/galaxy.model.migrate.rst
M doc/source/lib/galaxy.model.orm.rst
M doc/source/lib/galaxy.model.rst
M doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
M doc/source/lib/galaxy.model.tool_shed_install.rst
M doc/source/lib/galaxy.objectstore.rst
M doc/source/lib/galaxy.openid.rst
M doc/source/lib/galaxy.quota.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.sample_tracking.rst
M doc/source/lib/galaxy.security.rst
R doc/source/lib/galaxy.tags.rst
M doc/source/lib/galaxy.tools.actions.rst
A doc/source/lib/galaxy.tools.cwl.rst
M doc/source/lib/galaxy.tools.data.rst
M doc/source/lib/galaxy.tools.data_manager.rst
A doc/source/lib/galaxy.tools.deps.container_resolvers.rst
A doc/source/lib/galaxy.tools.deps.mulled.rst
M doc/source/lib/galaxy.tools.deps.resolvers.rst
M doc/source/lib/galaxy.tools.deps.rst
M doc/source/lib/galaxy.tools.filters.rst
M doc/source/lib/galaxy.tools.imp_exp.rst
M doc/source/lib/galaxy.tools.linters.rst
A doc/source/lib/galaxy.tools.locations.rst
M doc/source/lib/galaxy.tools.parameters.rst
M doc/source/lib/galaxy.tools.parser.rst
M doc/source/lib/galaxy.tools.rst
M doc/source/lib/galaxy.tools.search.rst
M doc/source/lib/galaxy.tools.toolbox.filters.rst
M doc/source/lib/galaxy.tools.toolbox.lineages.rst
M doc/source/lib/galaxy.tools.toolbox.rst
M doc/source/lib/galaxy.tools.util.galaxyops.rst
M doc/source/lib/galaxy.tools.util.rst
A doc/source/lib/galaxy.tools.verify.asserts.rst
A doc/source/lib/galaxy.tools.verify.rst
A doc/source/lib/galaxy.tours.rst
M doc/source/lib/galaxy.util.backports.rst
M doc/source/lib/galaxy.util.log.rst
M doc/source/lib/galaxy.util.pastescript.rst
M doc/source/lib/galaxy.util.rst
M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
M doc/source/lib/galaxy.visualization.data_providers.rst
M doc/source/lib/galaxy.visualization.genome.rst
M doc/source/lib/galaxy.visualization.plugins.rst
M doc/source/lib/galaxy.visualization.rst
M doc/source/lib/galaxy.visualization.tracks.rst
M doc/source/lib/galaxy.web.base.controllers.rst
M doc/source/lib/galaxy.web.base.rst
M doc/source/lib/galaxy.web.framework.helpers.rst
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/lib/galaxy.web.framework.rst
M doc/source/lib/galaxy.web.proxy.rst
M doc/source/lib/galaxy.web.rst
M doc/source/lib/galaxy.web.security.rst
A doc/source/lib/galaxy.web.stack.rst
A doc/source/lib/galaxy.webapps.galaxy.api.rst
M doc/source/lib/galaxy.webapps.galaxy.controllers.rst
M doc/source/lib/galaxy.webapps.galaxy.rst
M doc/source/lib/galaxy.webapps.reports.controllers.rst
M doc/source/lib/galaxy.webapps.reports.rst
M doc/source/lib/galaxy.webapps.rst
A doc/source/lib/galaxy.webapps.tool_shed.api.rst
M doc/source/lib/galaxy.webapps.tool_shed.controllers.rst
M doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst
M doc/source/lib/galaxy.webapps.tool_shed.framework.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.rst
M doc/source/lib/galaxy.webapps.tool_shed.rst
M doc/source/lib/galaxy.webapps.tool_shed.search.rst
M doc/source/lib/galaxy.webapps.tool_shed.security.rst
M doc/source/lib/galaxy.webapps.tool_shed.util.rst
A doc/source/lib/galaxy.webhooks.rst
M doc/source/lib/galaxy.work.rst
M doc/source/lib/galaxy.workflow.rst
M doc/source/lib/galaxy.workflow.schedulers.rst
M doc/source/lib/galaxy_ext.metadata.rst
M doc/source/lib/galaxy_ext.rst
M doc/source/lib/log_tempfile.rst
M doc/source/lib/psyco_full.rst
M doc/source/lib/tool_shed.capsule.rst
M doc/source/lib/tool_shed.dependencies.repository.rst
M doc/source/lib/tool_shed.dependencies.rst
M doc/source/lib/tool_shed.dependencies.tool.rst
M doc/source/lib/tool_shed.galaxy_install.datatypes.rst
M doc/source/lib/tool_shed.galaxy_install.grids.rst
M doc/source/lib/tool_shed.galaxy_install.metadata.rst
M doc/source/lib/tool_shed.galaxy_install.migrate.rst
M doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst
M doc/source/lib/tool_shed.galaxy_install.rst
M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst
M doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst
M doc/source/lib/tool_shed.galaxy_install.tools.rst
M doc/source/lib/tool_shed.galaxy_install.utility_containers.rst
M doc/source/lib/tool_shed.grids.rst
M doc/source/lib/tool_shed.managers.rst
M doc/source/lib/tool_shed.metadata.rst
M doc/source/lib/tool_shed.repository_types.rst
M doc/source/lib/tool_shed.rst
M doc/source/lib/tool_shed.tools.rst
M doc/source/lib/tool_shed.util.rst
M doc/source/lib/tool_shed.utility_containers.rst
M doc/source/project/organization.rst
M doc/source/releases/13.01_announce.rst
M doc/source/releases/13.02_announce.rst
M doc/source/releases/13.04_announce.rst
M doc/source/releases/13.06_announce.rst
M doc/source/releases/13.08_announce.rst
M doc/source/releases/13.11_announce.rst
M doc/source/releases/14.02_announce.rst
M doc/source/releases/14.04_announce.rst
M doc/source/releases/14.06_announce.rst
M doc/source/releases/14.08_announce.rst
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M doc/source/releases/15.01_announce.rst
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M doc/source/releases/16.04_announce.rst
M doc/source/releases/16.07_announce.rst
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A doc/source/releases/18.01_announce.rst
M doc/source/releases/index.rst
M doc/source/slideshow/architecture/galaxy_architecture.md
M lib/galaxy/__init__.py
M lib/galaxy/actions/admin.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/dataset_collections/builder.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.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/dataset_collections/types/__init__.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
A 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/chrominfo.py
R lib/galaxy/datatypes/converters/bam_to_bai.xml
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/bgzip.py
A lib/galaxy/datatypes/converters/biom1_to_biom2.xml
A lib/galaxy/datatypes/converters/biom2_to_biom1.xml
M lib/galaxy/datatypes/converters/fasta_to_len.py
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
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_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_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/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
M lib/galaxy/datatypes/coverage.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/chunk.py
M lib/galaxy/datatypes/dataproviders/column.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/decorators.py
M lib/galaxy/datatypes/dataproviders/exceptions.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/dataproviders/hierarchy.py
M lib/galaxy/datatypes/dataproviders/line.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/display_applications/parameters.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/graph.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/neo4j.py
M lib/galaxy/datatypes/ngsindex.py
A 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/set_metadata_tool.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.bcf
A lib/galaxy/datatypes/test/1.bcf_uncompressed
A lib/galaxy/datatypes/test/1.memepsp
A lib/galaxy/datatypes/test/1.ptkscmp
A lib/galaxy/datatypes/test/1.xls
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
A lib/galaxy/datatypes/test/test.fast5.tar
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M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/util/generic_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-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/parameters.py
M lib/galaxy/external_services/result_handlers/basic.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/datasets.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/data_transfer.py
M lib/galaxy/jobs/deferred/manual_data_transfer.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/cli.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/collectl/stats.py
M lib/galaxy/jobs/metrics/collectl/subsystems.py
M lib/galaxy/jobs/metrics/instrumenters/__init__.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
A lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/cli/__init__.py
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/splitters/basic.py
M lib/galaxy/jobs/splitters/multi.py
M lib/galaxy/jobs/stock_rules.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/annotatable.py
M lib/galaxy/managers/api_keys.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.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/context.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/deletable.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/lddas.py
M lib/galaxy/managers/libraries.py
A lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/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/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/base.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/check.py
M lib/galaxy/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/model/migrate/versions/0002_metadata_file_table.py
M lib/galaxy/model/migrate/versions/0003_security_and_libraries.py
M lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py
M lib/galaxy/model/migrate/versions/0007_sharing_histories.py
M lib/galaxy/model/migrate/versions/0008_galaxy_forms.py
M lib/galaxy/model/migrate/versions/0009_request_table.py
M lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py
M lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0012_user_address.py
M lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py
M lib/galaxy/model/migrate/versions/0014_pages.py
M lib/galaxy/model/migrate/versions/0015_tagging.py
M lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py
M lib/galaxy/model/migrate/versions/0017_library_item_indexes.py
M lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py
M lib/galaxy/model/migrate/versions/0019_request_library_folder.py
M lib/galaxy/model/migrate/versions/0020_library_upload_job.py
M lib/galaxy/model/migrate/versions/0021_user_prefs.py
M lib/galaxy/model/migrate/versions/0022_visualization_tables.py
M lib/galaxy/model/migrate/versions/0023_page_published_and_deleted_columns.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0025_user_info.py
M lib/galaxy/model/migrate/versions/0026_cloud_tables.py
M lib/galaxy/model/migrate/versions/0027_request_events.py
M lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py
M lib/galaxy/model/migrate/versions/0029_user_actions.py
M lib/galaxy/model/migrate/versions/0030_history_slug_column.py
M lib/galaxy/model/migrate/versions/0031_community_and_workflow_tags.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0034_page_user_share_association.py
M lib/galaxy/model/migrate/versions/0035_item_annotations_and_workflow_step_tags.py
M lib/galaxy/model/migrate/versions/0036_add_deleted_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0037_samples_library.py
M lib/galaxy/model/migrate/versions/0038_add_inheritable_column_to_library_template_assoc_tables.py
M lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_table.py
M lib/galaxy/model/migrate/versions/0040_page_annotations.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0043_visualization_sharing_tagging_annotating.py
M lib/galaxy/model/migrate/versions/0044_add_notify_column_to_request_table.py
M lib/galaxy/model/migrate/versions/0045_request_type_permissions_table.py
M lib/galaxy/model/migrate/versions/0046_post_job_actions.py
M lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py
M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py
M lib/galaxy/model/migrate/versions/0049_api_keys_table.py
M lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py
M lib/galaxy/model/migrate/versions/0051_imported_col_for_jobs_table.py
M lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py
M lib/galaxy/model/migrate/versions/0053_item_ratings.py
M lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py
M lib/galaxy/model/migrate/versions/0055_add_pja_assoc_for_jobs.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0057_request_notify.py
M lib/galaxy/model/migrate/versions/0058_history_import_export.py
M lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py
M lib/galaxy/model/migrate/versions/0060_history_archive_import.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0062_user_openid_table.py
M lib/galaxy/model/migrate/versions/0063_sequencer_table.py
M lib/galaxy/model/migrate/versions/0064_add_run_and_sample_run_association_tables.py
M lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py
M lib/galaxy/model/migrate/versions/0066_deferred_job_and_transfer_job_tables.py
M lib/galaxy/model/migrate/versions/0067_populate_sequencer_table.py
M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py
M lib/galaxy/model/migrate/versions/0069_rename_sequencer_form_type.py
M lib/galaxy/model/migrate/versions/0070_add_info_column_to_deferred_job_table.py
M lib/galaxy/model/migrate/versions/0071_add_history_and_workflow_to_sample.py
M lib/galaxy/model/migrate/versions/0072_add_pid_and_socket_columns_to_transfer_job_table.py
M lib/galaxy/model/migrate/versions/0073_add_ldda_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0074_add_purged_column_to_library_dataset_table.py
M lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py
M lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py
M lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py
M lib/galaxy/model/migrate/versions/0080_quota_tables.py
M lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py
M lib/galaxy/model/migrate/versions/0082_add_tool_shed_repository_table.py
M lib/galaxy/model/migrate/versions/0083_add_prepare_files_to_task.py
M lib/galaxy/model/migrate/versions/0084_add_ldda_id_to_implicit_conversion_table.py
M lib/galaxy/model/migrate/versions/0085_add_task_info.py
M lib/galaxy/model/migrate/versions/0086_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0087_tool_id_guid_map_table.py
M lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py
M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py
M lib/galaxy/model/migrate/versions/0090_add_tool_shed_repository_table_columns.py
M lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py
M lib/galaxy/model/migrate/versions/0092_add_migrate_tools_table.py
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M lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py
M lib/galaxy/model/migrate/versions/0095_hda_subsets.py
M lib/galaxy/model/migrate/versions/0096_openid_provider.py
M lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py
M lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py
M lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py
M lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py
M lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py
M lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py
M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py
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M lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py
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M lib/galaxy/model/migrate/versions/0111_add_job_destinations.py
M lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py
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M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
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M lib/galaxy/model/migrate/versions/0117_add_user_activation.py
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M templates/display_common.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/js-app.mako
M templates/sharing_base.mako
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M templates/webapps/galaxy/dataset/display.mako
R templates/webapps/galaxy/dataset/edit_attributes.mako
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M templates/webapps/galaxy/galaxy.panels.mako
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R templates/webapps/galaxy/history/list_published.mako
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R templates/webapps/galaxy/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
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M templates/webapps/galaxy/page/editor.mako
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R templates/webapps/galaxy/page/list_published.mako
R templates/webapps/galaxy/page/select_items_grid.mako
M templates/webapps/galaxy/requests/common/common.mako
M templates/webapps/galaxy/root/tool_runner.mako
R templates/webapps/galaxy/tracks/add_to_viz.mako
R templates/webapps/galaxy/tracks/add_tracks.mako
R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako
R templates/webapps/galaxy/tracks/history_select_grid.mako
R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako
R templates/webapps/galaxy/visualization/list.mako
R templates/webapps/galaxy/visualization/list_published.mako
M templates/webapps/galaxy/workflow/build_from_current_history.mako
R templates/webapps/galaxy/workflow/configure_menu.mako
M templates/webapps/galaxy/workflow/editor.mako
R templates/webapps/galaxy/workflow/import.mako
R templates/webapps/galaxy/workflow/list.mako
R templates/webapps/galaxy/workflow/list_for_run.mako
R templates/webapps/galaxy/workflow/list_published.mako
R templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/base_panels.mako
M templates/webapps/tool_shed/admin/center.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako
A templates/webapps/tool_shed/admin/dataset_security/group/group_rename.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako
A templates/webapps/tool_shed/admin/dataset_security/role/role_rename.mako
A templates/webapps/tool_shed/admin/user/reset_password.mako
A templates/webapps/tool_shed/admin/user/user.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/repository/common.mako
R templates/webapps/tool_shed/repository/grid.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/1.sam.gz
A test-data/5_Ig-like.gff
A test-data/bad.html.gz
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
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A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
A test-data/random-file
A test-data/test.vcf.gz
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datasets.py
M test/api/test_datatypes.py
M test/api/test_framework.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_history_contents_provenance.py
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_page_revisions.py
M test/api/test_pages.py
M test/api/test_search.py
M test/api/test_tool_data.py
M test/api/test_tools.py
M test/api/test_tours.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflow_extraction.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/api_asserts.py
M test/base/api_util.py
M test/base/driver_util.py
M test/base/instrument.py
M test/base/interactor.py
M test/base/nose_util.py
M test/base/populators.py
R test/base/test_db_util.py
A test/base/testcase.py
M test/base/tool_shed_util.py
R test/base/twilltestcase.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
M test/casperjs/casperjs_runner.py
M test/casperjs/server_env.py
R test/functional/database_contexts.py
M test/functional/test_data_managers.py
R test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/code_file.py
A test/functional/tools/collection_creates_dynamic_nested_fail.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json.xml
A test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
A test/functional/tools/collection_creates_list_fail.xml
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
A test/functional/tools/identifier_source.xml
M test/functional/tools/metadata.xml
A test/functional/tools/mulled_example_multi_versionless.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/tools/tool_provided_metadata_1.xml
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A test/functional/tools/vcf_bgzip.xml
A test/functional/twilltestcase.py
M test/functional/webhooks/phdcomics/helper/__init__.py
M test/functional/webhooks/trans_object/helper/__init__.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/driver_factory.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/sizzle.py
A test/integration/test_config_options_users.py
A test/integration/test_data_manager_table_reload.py
M test/integration/test_maximum_worklfow_invocation_duration.py
M test/integration/test_resolvers.py
A test/integration/test_upload_configuration_options.py
M test/integration/test_workflow_handler_configuration.py
A test/integration/tool_sheds_conf.xml
M test/manual/workflows_scaling.py
M test/qunit/test-data/bootstrapped.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/ui_tests.html
M test/qunit/tests/ui_tests.js
M test/selenium_tests/framework.py
A test/selenium_tests/test_custom_builds.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_login.py
A test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_registration.py
A test/selenium_tests/test_saved_histories.py
A test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_0000_basic_repository_features.py
M test/shed_functional/functional/test_0010_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_0020_basic_repository_dependencies.py
M test/shed_functional/functional/test_0030_repository_dependency_revisions.py
M test/shed_functional/functional/test_0040_repository_circular_dependencies.py
M test/shed_functional/functional/test_0050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_0060_workflows.py
M test/shed_functional/functional/test_0070_invalid_tool.py
M test/shed_functional/functional/test_0080_advanced_circular_dependencies.py
M test/shed_functional/functional/test_0090_tool_search.py
M test/shed_functional/functional/test_0100_complex_repository_dependencies.py
M test/shed_functional/functional/test_0110_invalid_simple_repository_dependencies.py
M test/shed_functional/functional/test_0120_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_0130_datatype_converters.py
M test/shed_functional/functional/test_0140_tool_help_images.py
M test/shed_functional/functional/test_0150_prior_installation_required.py
M test/shed_functional/functional/test_0160_circular_prior_installation_required.py
M test/shed_functional/functional/test_0170_complex_prior_installation_required.py
M test/shed_functional/functional/test_0300_reset_all_metadata.py
M test/shed_functional/functional/test_0310_hg_api_features.py
M test/shed_functional/functional/test_0400_repository_component_reviews.py
M test/shed_functional/functional/test_0410_repository_component_review_access_control.py
M test/shed_functional/functional/test_0420_citable_urls_for_repositories.py
M test/shed_functional/functional/test_0430_browse_utilities.py
M test/shed_functional/functional/test_0440_deleting_dependency_definitions.py
M test/shed_functional/functional/test_0460_upload_to_repository.py
M test/shed_functional/functional/test_0470_tool_dependency_repository_type.py
M test/shed_functional/functional/test_0480_tool_dependency_xml_verification.py
M test/shed_functional/functional/test_0490_export_import_repositories.py
M test/shed_functional/functional/test_0500_export_repository_simple_dependency.py
M test/shed_functional/functional/test_0510_export_import_repository_complex_dependencies.py
M test/shed_functional/functional/test_0520_import_export_circular_dependencies.py
M test/shed_functional/functional/test_0530_repository_admin_feature.py
M test/shed_functional/functional/test_0540_get_all_metadata_from_api.py
M test/shed_functional/functional/test_0550_metadata_updated_dependencies.py
M test/shed_functional/functional/test_1000_install_basic_repository.py
M test/shed_functional/functional/test_1010_install_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1020_install_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1030_install_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1040_install_repository_basic_circular_dependencies.py
M test/shed_functional/functional/test_1050_circular_dependencies_4_levels.py
M test/shed_functional/functional/test_1060_install_repository_with_workflow.py
M test/shed_functional/functional/test_1070_invalid_tool.py
M test/shed_functional/functional/test_1080_advanced_circular_dependency_installation.py
M test/shed_functional/functional/test_1090_repository_dependency_handling.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1110_install_tool_from_tool_search.py
M test/shed_functional/functional/test_1120_install_repository_with_complex_dependencies.py
M test/shed_functional/functional/test_1130_install_repository_with_invalid_repository_dependency.py
M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py
M test/shed_functional/functional/test_1150_datatype_converters.py
M test/shed_functional/functional/test_1160_tool_help_images.py
M test/shed_functional/functional/test_1170_prior_installation_required.py
M test/shed_functional/functional/test_1180_circular_prior_installation_required.py
M test/shed_functional/functional/test_1190_complex_prior_installation_required.py
M test/shed_functional/functional/test_1200_uninstall_and_reinstall_basic_repository.py
M test/shed_functional/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
M test/shed_functional/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
M test/shed_functional/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
M test/shed_functional/functional/test_1300_reset_all_metadata.py
M test/shed_functional/functional/test_1400_review_migration_stages.py
M test/shed_functional/functional/test_1410_update_manager.py
M test/shed_functional/functional/test_1420_tool_dependency_environment_inheritance.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
M test/shed_functional/functional/test_1440_missing_env_sh_files.py
M test/shed_functional/functional/test_1450_installing_datatypes_sniffers.py
M test/shed_functional/functional/test_1460_data_managers.py
M test/shed_functional/functional/test_1470_updating_installed_repositories.py
M test/shed_functional/functional_tests.py
A test/unit/config/1607_root_filters/config/galaxy.ini
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A test/unit/config/1607_root_samples/config/tool_shed.ini
A test/unit/config/test_config_manage.py
M test/unit/dataset_collections/test_matching.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/datatypes/test_data.py
A test/unit/jobs/conditional_runners_job_conf.xml
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/test_command_factory.py
M test/unit/jobs/test_datasets.py
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_rule_helper.py
M test/unit/jobs/test_rules/10_site.py
M test/unit/jobs/test_runner_local.py
M test/unit/jobs/test_runner_params.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_fabric_util.py
A test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_td_common_util.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_galaxy_transactions.py
A test/unit/test_remote_shell.py
M test/unit/test_routes.py
M test/unit/test_security_helper.py
M test/unit/test_sqlite_utils.py
M test/unit/test_topsort.py
M test/unit/tools/filter_modules/filtermod.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_citations.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
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M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
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M test/unit/tools/test_select_parameters.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_panel.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools/test_watcher.py
M test/unit/tools/test_wrappers.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/unittest_utils/utility.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/base/test_HookPluginManager.py
M test/unit/web/base/test_PageServingPluginManager.py
M test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M test/unit/workflows/workflow_support.py
M tool_list.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/hbvar_filter.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/add_scores.py
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/filters/axt_to_lav.py
M tools/filters/axt_to_lav_code.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff/gtf_filter_by_attribute_values_list.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/grep.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joinWrapper.py
M tools/filters/joiner.xml
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/random_lines_two_pass.py
M tools/filters/randomlines.py
M tools/filters/secure_hash_message_digest.py
M tools/filters/sorter.py
M tools/filters/trimmer.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/filters/wc_gnu.xml
M tools/filters/wiggle_to_simple.py
M tools/genomespace/genomespace_exporter.py
M tools/genomespace/genomespace_exporter.xml
M tools/genomespace/genomespace_file_browser.py
R tools/genomespace/genomespace_file_browser_dev.xml
R tools/genomespace/genomespace_file_browser_prod.xml
R tools/genomespace/genomespace_file_browser_test.xml
M tools/genomespace/genomespace_importer.py
M tools/genomespace/genomespace_importer.xml
A tools/genomespace/genomespace_push.xml
M tools/maf/interval2maf.py
M tools/maf/interval_maf_to_merged_fasta.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_split_by_species.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/maf_to_bed_code.py
M tools/maf/maf_to_fasta_concat.py
M tools/maf/maf_to_fasta_multiple_sets.py
M tools/maf/maf_to_interval.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/meme/fimo_wrapper.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/fastq_conversions.py
M tools/next_gen_conversion/fastq_gen_conv.py
M tools/next_gen_conversion/solid2fastq.py
M tools/next_gen_conversion/solid_to_fastq.py
M tools/ngs_simulation/ngs_simulation.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg.xml
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_assembly/velveth_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/sr_mapping/srma_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/visualization/LAJ.py
M tools/visualization/LAJ_code.py
M tox.ini
Log Message:
-----------
Merge branch 'release_17.09'
Commit: cd1454c40a43ad9da3d59e6ba8359318fc772c43
https://github.com/galaxyproject/galaxy/commit/cd1454c40a43ad9da3d59e6ba835…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Log Message:
-----------
Merge pull request #5141 from jmchilton/master
[17.09] Re-merge master into release_17.09.
Compare: https://github.com/galaxyproject/galaxy/compare/b0c03240fd96...cd1454c40a43
1
0
[galaxyproject/galaxy] d24b54: Migrate documentation for setting up a production ...
by GitHub 06 Dec '17
by GitHub 06 Dec '17
06 Dec '17
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: d24b545d70020a26ae3a51a7325fdbc57b6384dd
https://github.com/galaxyproject/galaxy/commit/d24b545d70020a26ae3a51a7325f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-05 (Tue, 05 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Migrate documentation for setting up a production instance to Galaxy.
This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).
This content currently includes:
- the production configuration page
- the cluster configuration page
- the job configuration page
- the scaling information page
- the ftp configuration page
- the top-level nginx page (for external auth content still linking out to the hub)
- the top-level apache page (for external auth content still linking out to the hub)
- the job metrics configuration page
Includes small tweaks to sphinx documentation generation.
- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs.
- Use AutoStructify for better Markdown integration.
Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:
- Update the job configuration page with information about XML macros.
- Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore).
- Updated list of dynamic job runner configuration parameters.
- Mention the ``raw`` attribute for ``env`` directives in the job configuration page.
- Mention the ``total_walltime`` limit added in #3217.
- Drop mentions of older URL-based job conf configuration stuff.
- Mention newer Local and Paramiko based shell runners in CLI section.
- Mention newer slurm job styles in CLI section.
- Improved Pulsar links.
- Fix dataset security link in Apache display sites config.
- Update job metrics page to link to a new Github issue instead of old Trello issues.
Commit: befa077cc444115e0cac738c2bd3ee786f7425d2
https://github.com/galaxyproject/galaxy/commit/befa077cc444115e0cac738c2bd3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M doc/source/admin/jobs.md
Log Message:
-----------
Rework headings in jobs docs.
Thanks to comment from @erasche review.
Commit: b0c03240fd96ace2b25680e753fed0237264ec98
https://github.com/galaxyproject/galaxy/commit/b0c03240fd96ace2b25680e753fe…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
A doc/source/admin/cluster.md
M doc/source/admin/index.rst
A doc/source/admin/jobs.md
A doc/source/admin/production.md
A doc/source/admin/scaling.md
A doc/source/admin/special_topics/apache.md
A doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
A doc/source/admin/special_topics/job_metrics.md
A doc/source/admin/special_topics/nginx.md
M doc/source/conf.py
Log Message:
-----------
Merge pull request #5135 from jmchilton/17.09_admin_docs
[17.09] Migrate documentation for setting up a production instance to Galaxy.
Compare: https://github.com/galaxyproject/galaxy/compare/22aa02f59496...b0c03240fd96
1
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Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 28cdb6d165293060458e5336d7ab4b9972c0a826
https://github.com/galaxyproject/galaxy/commit/28cdb6d165293060458e5336d7ab…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Postpone depends_list generation
No need to calculate it if a converted dataset already exists.
Commit: 4d30b4f9cc5c580637af3a1bd9aaca8932d465f1
https://github.com/galaxyproject/galaxy/commit/4d30b4f9cc5c580637af3a1bd9aa…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths:
M lib/galaxy/model/__init__.py
Log Message:
-----------
Merge pull request #5137 from nsoranzo/datatype_conversion_fixes
Postpone depends_list generation
Compare: https://github.com/galaxyproject/galaxy/compare/211121877c3a...4d30b4f9cc5c
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[galaxyproject/galaxy] 0dfe73: Determine dynamically if an extension corresponds ...
by GitHub 05 Dec '17
by GitHub 05 Dec '17
05 Dec '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0dfe73a54cebb1e4fd7a02d9ff05ca585d034244
https://github.com/galaxyproject/galaxy/commit/0dfe73a54cebb1e4fd7a02d9ff05…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-12-01 (Fri, 01 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M tools/data_source/upload.py
Log Message:
-----------
Determine dynamically if an extension corresponds to an unsniffable binary datatype
Remove the need to call `Binary.register_unsniffable_binary_ext()` for
each unsniffable binary datatype.
Fix https://github.com/galaxyproject/galaxy/issues/3441 , where the upload
of files of a datatype defined in datatypes_conf.xml as subclass of an
unsniffable binary datatype ended up with "The uploaded binary file
contains inappropriate content" because it was not possible to register the
subclassed datatype as unsniffable.
Also remove unused `stop_err()` function in upload.py .
Commit: 211121877c3a579e3c9cbd05c0933017177f26a8
https://github.com/galaxyproject/galaxy/commit/211121877c3a579e3c9cbd05c093…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-12-05 (Tue, 05 Dec 2017)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sniff.py
M tools/data_source/upload.py
Log Message:
-----------
Merge pull request #5109 from nsoranzo/deprecate_register_unsniffable_binary_ext
Determine dynamically if an extension corresponds to an unsniffable binary datatype
Compare: https://github.com/galaxyproject/galaxy/compare/f09944a8229b...211121877c3a
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