January 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6cb9d6: Fix Galaxy instance startup error
by GitHub 14 Jan '18

14 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6cb9d664dee2af178f179e9fc3f528710c5d4507 https://github.com/galaxyproject/galaxy/commit/6cb9d664dee2af178f179e9fc3f5… Author: anup kumar <anup.rulez(a)gmail.com> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Fix Galaxy instance startup error Commit: 9ac5052d7acfd0099ecfafd7109bb30b6a1e5145 https://github.com/galaxyproject/galaxy/commit/9ac5052d7acfd0099ecfafd7109b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-14 (Sun, 14 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5306 from bgruening/structure_view_history Fix Galaxy instance startup error Compare: https://github.com/galaxyproject/galaxy/compare/199457f23bf6...9ac5052d7acf

1 0

[galaxyproject/galaxy] a847db: Fix tool report submission
by GitHub 12 Jan '18

12 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a847dbd3d5e312b13cfe8a90844c8f88d3aedc78 https://github.com/galaxyproject/galaxy/commit/a847dbd3d5e312b13cfe8a90844c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Fix tool report submission Commit: a6e9504dde8b5c96f6f5fc183c56d9458b996588 https://github.com/galaxyproject/galaxy/commit/a6e9504dde8b5c96f6f5fc183c56… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #5303 from mvdbeek/sentry_hotfix [17.09] Fix tool report submission with sentry Compare: https://github.com/galaxyproject/galaxy/compare/a81f3e4e8c5f...a6e9504dde8b

1 0

[galaxyproject/galaxy] a70ecd: Fix common_startup.sh bashisms
by GitHub 12 Jan '18

12 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a70ecd0147bb178b90b820d4c5cac0caa86152ab https://github.com/galaxyproject/galaxy/commit/a70ecd0147bb178b90b820d4c5ca… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Fix common_startup.sh bashisms Introduced in commit 45a25a1b8bd182cc6dff2926974681ef1bf4fc6f . This was causing this error on the `dev` branch on Ubuntu (which uses `dash`): ``` $ ./run.sh ./scripts/common_startup.sh: 69: [: dev: unexpected operator Activating virtualenv at .venv ... ``` instead of exiting with the "The Galaxy client build is out of date." message. Commit: 199457f23bf66fab7a1ca6cf86bbb215274d983c https://github.com/galaxyproject/galaxy/commit/199457f23bf66fab7a1ca6cf86bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-12 (Fri, 12 Jan 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #5304 from nsoranzo/fix_common_startup.sh Fix common_startup.sh bashisms Compare: https://github.com/galaxyproject/galaxy/compare/a2f8ff21fdc2...199457f23bf6

1 0

[galaxyproject/galaxy] cf1557: Improve the migration message when having to downg...
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cf155744662a2b6b0ce7d751f7d1429929b9a764 https://github.com/galaxyproject/galaxy/commit/cf155744662a2b6b0ce7d751f7d1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Improve the migration message when having to downgrade the database Commit: 58cda0ddd1663c16ba9b4772d9d2334cb4d45543 https://github.com/galaxyproject/galaxy/commit/58cda0ddd1663c16ba9b4772d9d2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Slight wording tweak to migration message Commit: a2f8ff21fdc240e12c0dff2d2eb95ff7bbdc8d49 https://github.com/galaxyproject/galaxy/commit/a2f8ff21fdc240e12c0dff2d2eb9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/model/migrate/check.py Log Message: ----------- Merge pull request #5299 from mvdbeek/improve_downgrade_message Improve the migration message when having to downgrade the database Compare: https://github.com/galaxyproject/galaxy/compare/79651a108011...a2f8ff21fdc2

1 0

[galaxyproject/galaxy] bb39b7: Provide UI collection output information for subwo...
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bb39b7d60b39eeae7f112edb42d9563731a725bf https://github.com/galaxyproject/galaxy/commit/bb39b7d60b39eeae7f112edb42d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Provide UI collection output information for subworkflows. This fixes #5158 and should provide more correct extension based connection information as well. Includes a backport of #4346 which fixes #3120. Commit: d1510c739492cf1e7b9d0e2d793dfb4d18d91537 https://github.com/galaxyproject/galaxy/commit/d1510c739492cf1e7b9d0e2d793d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-01 (Mon, 01 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5172 from jmchilton/1705_subworkflow_collection_outputs [17.05] Provide UI collection output information for subworkflows. Commit: a19596e3eacf63e749352f583be8774d43795d79 https://github.com/galaxyproject/galaxy/commit/a19596e3eacf63e749352f583be8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix dataset-model's edit url Commit: 9aabaa68594421e920ed6d1ac1d287e561453d8b https://github.com/galaxyproject/galaxy/commit/9aabaa68594421e920ed6d1ac1d2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-model.js Log Message: ----------- Build client Commit: 40f9c6bb858da82e21679281d3cc644271f53eb8 https://github.com/galaxyproject/galaxy/commit/40f9c6bb858da82e21679281d3cc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-model.js M static/maps/mvc/dataset/dataset-model.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/dataset/dataset-model.js Log Message: ----------- Merge pull request #5289 from dannon/dataset_edit_fix [17.09] Fix dataset edit link Commit: 27c9fff8b9333d67c039cdbd5c7f1840f095633d https://github.com/galaxyproject/galaxy/commit/27c9fff8b9333d67c039cdbd5c7f… Author: NCEichner <norbert.eichner(a)ur.de> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- #5187 In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4" Commit: 201c6ca8812b243d7ff824df58a3b2fd64a88289 https://github.com/galaxyproject/galaxy/commit/201c6ca8812b243d7ff824df58a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5298 from nsoranzo/release_17.09_backport_5233 [17.09] Backport #5233 Commit: a81f3e4e8c5fb06c2cd33569380a188b44a9da8a https://github.com/galaxyproject/galaxy/commit/a81f3e4e8c5fb06c2cd33569380a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Conflicts: lib/galaxy/workflow/modules.py Commit: 79651a1080112df0826cc74130f65bd793d0fdc8 https://github.com/galaxyproject/galaxy/commit/79651a1080112df0826cc74130f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/db8721e6b869...79651a108011

1 0

[galaxyproject/galaxy] bb39b7: Provide UI collection output information for subwo...
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: bb39b7d60b39eeae7f112edb42d9563731a725bf https://github.com/galaxyproject/galaxy/commit/bb39b7d60b39eeae7f112edb42d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-12-08 (Fri, 08 Dec 2017) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Provide UI collection output information for subworkflows. This fixes #5158 and should provide more correct extension based connection information as well. Includes a backport of #4346 which fixes #3120. Commit: d1510c739492cf1e7b9d0e2d793dfb4d18d91537 https://github.com/galaxyproject/galaxy/commit/d1510c739492cf1e7b9d0e2d793d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-01 (Mon, 01 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #5172 from jmchilton/1705_subworkflow_collection_outputs [17.05] Provide UI collection output information for subworkflows. Commit: a81f3e4e8c5fb06c2cd33569380a188b44a9da8a https://github.com/galaxyproject/galaxy/commit/a81f3e4e8c5fb06c2cd33569380a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'release_17.05' into release_17.09 Conflicts: lib/galaxy/workflow/modules.py Compare: https://github.com/galaxyproject/galaxy/compare/201c6ca8812b...a81f3e4e8c5f

1 0

[galaxyproject/galaxy] 27c9ff: #5187
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 27c9fff8b9333d67c039cdbd5c7f1840f095633d https://github.com/galaxyproject/galaxy/commit/27c9fff8b9333d67c039cdbd5c7f… Author: NCEichner <norbert.eichner(a)ur.de> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- #5187 In order to get rid of the conda error described in #5187 I raised the version number beginning from which conda is allowed to use the '--offline' parameter again to "4.4" Commit: 201c6ca8812b243d7ff824df58a3b2fd64a88289 https://github.com/galaxyproject/galaxy/commit/201c6ca8812b243d7ff824df58a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #5298 from nsoranzo/release_17.09_backport_5233 [17.09] Backport #5233 Compare: https://github.com/galaxyproject/galaxy/compare/40f9c6bb858d...201c6ca8812b

1 0

[galaxyproject/galaxy] 5c4c25: Mention how to specify the config file location
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c4c25b63d574562ea93687c95e654d5571b5710 https://github.com/galaxyproject/galaxy/commit/5c4c25b63d574562ea93687c95e6… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M scripts/db_shell.py Log Message: ----------- Mention how to specify the config file location and how to do that when using ipython. Commit: db8721e6b869548039b7a4c40b7e49575d800fbb https://github.com/galaxyproject/galaxy/commit/db8721e6b869548039b7a4c40b7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M scripts/db_shell.py Log Message: ----------- Merge pull request #5297 from mvdbeek/db_shell_doc_update Mention how to specify the config file location Compare: https://github.com/galaxyproject/galaxy/compare/c7581f867de0...db8721e6b869

1 0

[galaxyproject/galaxy] ad925d: add infernal-cm datatype
by GitHub 11 Jan '18

11 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad925ddfcaa205918aac2f4fb48e4b6f93edf29c https://github.com/galaxyproject/galaxy/commit/ad925ddfcaa205918aac2f4fb48e… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/infernal.py Log Message: ----------- add infernal-cm datatype Commit: 772bab983d28235e2f16c2e85803309917a1a179 https://github.com/galaxyproject/galaxy/commit/772bab983d28235e2f16c2e85803… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- simplify sniff Commit: ad3f54676943e57aa089358c2b4ec8163e824220 https://github.com/galaxyproject/galaxy/commit/ad3f54676943e57aa089358c2b4e… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- no cm count Commit: 3b394e10c9ffa13e0de1c6163c1012053d005c27 https://github.com/galaxyproject/galaxy/commit/3b394e10c9ffa13e0de1c6163c10… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- lint py3 Commit: 2c083e24e8716c8c61fab2a213d25ae928b07210 https://github.com/galaxyproject/galaxy/commit/2c083e24e8716c8c61fab2a213d2… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- lint py3 fix Commit: 0f8fbed83b4dae66529802fe98fa83737375751d https://github.com/galaxyproject/galaxy/commit/0f8fbed83b4dae66529802fe98fa… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- reorder import Commit: 22072a6cdb89b4a87b9e81274485c5ef7f2e94ee https://github.com/galaxyproject/galaxy/commit/22072a6cdb89b4a87b9e81274485… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-10 (Fri, 10 Nov 2017) Changed paths: M lib/galaxy/datatypes/infernal.py Log Message: ----------- minor reorders Commit: f52c5de5fb838e2dac6d447605db020752332639 https://github.com/galaxyproject/galaxy/commit/f52c5de5fb838e2dac6d447605db… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M config/datatypes_conf.xml.sample R lib/galaxy/datatypes/infernal.py M lib/galaxy/datatypes/msa.py Log Message: ----------- merge infernal into msa Commit: f33ee573e9b15f1479e5ab36facdcc7032a3264b https://github.com/galaxyproject/galaxy/commit/f33ee573e9b15f1479e5ab36facd… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-11 (Sat, 11 Nov 2017) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- minor fix Commit: 5cb1cb5ec20107a95755e1b6bcb69909878d002d https://github.com/galaxyproject/galaxy/commit/5cb1cb5ec20107a95755e1b6bcb6… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2017-11-17 (Fri, 17 Nov 2017) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Rename class, add CM version Commit: 20278b8b31ec15bd21f3ae8ff620472644a11b41 https://github.com/galaxyproject/galaxy/commit/20278b8b31ec15bd21f3ae8ff620… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm Log Message: ----------- add unit-test, fix class name Commit: 86955b4b3c907412916519a75ae30eca86ed8abf https://github.com/galaxyproject/galaxy/commit/86955b4b3c907412916519a75ae3… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- remove split for cm Commit: a73d566f1fa812e4e8ce4c32baa61647e689b5ac https://github.com/galaxyproject/galaxy/commit/a73d566f1fa812e4e8ce4c32baa6… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Dynamically set cm_version Commit: 5c415e6855987ac87bdc4318cd5e5ed512811496 https://github.com/galaxyproject/galaxy/commit/5c415e6855987ac87bdc4318cd5e… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/flake8_lint_include_list.txt R .ci/flake8_wrapper_imports.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md 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/history-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/Message.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/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/layout/generic-nav-view.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/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.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-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-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-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/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.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 A client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-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-dataset-view.js M client/galaxy/scripts/mvc/library/library-folderlist-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-libraryrow-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/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-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-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/ui/ui-slider.js M client/galaxy/scripts/mvc/ui/ui-tabs.js M client/galaxy/scripts/mvc/ui/ui-thumbnails.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js 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/visualization/visualization-model.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.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/nls/zh/locale.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/qunit/assets/base.css A client/galaxy/scripts/qunit/test-app.js A client/galaxy/scripts/qunit/test-data/bootstrapped.js A client/galaxy/scripts/qunit/test-data/fakeserver.js A client/galaxy/scripts/qunit/test-data/job-dag-1.js A client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js A client/galaxy/scripts/qunit/test.js A client/galaxy/scripts/qunit/tests/form_tests.js A client/galaxy/scripts/qunit/tests/galaxy_app_base_tests.js A client/galaxy/scripts/qunit/tests/graph_tests.js A client/galaxy/scripts/qunit/tests/hda_base_tests.js A client/galaxy/scripts/qunit/tests/history_contents_model_tests.js A client/galaxy/scripts/qunit/tests/job_dag_tests.js A client/galaxy/scripts/qunit/tests/list_of_pairs_collection_creator_tests.js A client/galaxy/scripts/qunit/tests/masthead_tests.js A client/galaxy/scripts/qunit/tests/metrics_logger_tests.js A client/galaxy/scripts/qunit/tests/modal_tests.js A client/galaxy/scripts/qunit/tests/page_tests.js A client/galaxy/scripts/qunit/tests/popover_tests.js A client/galaxy/scripts/qunit/tests/ui_tests.js A client/galaxy/scripts/qunit/tests/upload_dialog_tests.js A client/galaxy/scripts/qunit/tests/utils_tests.js A client/galaxy/scripts/qunit/tests/workflow_editor_tests.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/utils/ajax-queue.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/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 M client/galaxy/style/less/base.less M client/galaxy/style/less/dataset.less M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less M client/galaxy/style/less/list-item.less M client/galaxy/style/less/ui.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js M client/gulpfile.js A client/karma.config.js M client/package.json R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js 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/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/openid_conf.xml.sample A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample A config/plugins/interactive_environments/askomics/config/askomics.ini.sample A config/plugins/interactive_environments/askomics/config/askomics.xml A config/plugins/interactive_environments/askomics/static/js/askomics.js A config/plugins/interactive_environments/askomics/templates/askomics.mako M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.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/templates/charts.mako 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/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M config/user_preferences_extra_conf.yml.sample M config/workflow_schedulers_conf.xml.sample M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py 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/api/quickstart.rst M doc/source/conf.py M doc/source/releases/17.09_announce.rst 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 A lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/auth/__init__.py M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/auth/providers/pam_auth.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.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/type_description.py M lib/galaxy/dataset_collections/types/list.py M lib/galaxy/dataset_collections/types/paired.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/converters/bgzip.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/dataproviders/dataset.py M lib/galaxy/datatypes/display_applications/application.py M lib/galaxy/datatypes/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/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/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf A lib/galaxy/datatypes/test/1.vcf.gz A lib/galaxy/datatypes/test/2.cram A lib/galaxy/datatypes/test/2.shuffled.bam A lib/galaxy/datatypes/test/454Score.pdf A lib/galaxy/datatypes/test/linkstudies.allegro_fparam A lib/galaxy/datatypes/test/linkstudies.alohomora_gts A lib/galaxy/datatypes/test/linkstudies.linkage_datain A lib/galaxy/datatypes/test/linkstudies.linkage_map A lib/galaxy/datatypes/test/matrix.cool M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.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/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 R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/update.sh 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/forms/forms.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.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/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/processes.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/meminfo.py M lib/galaxy/jobs/output_checker.py M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/chronos.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/state_handlers/resubmit.py M lib/galaxy/jobs/runners/util/__init__.py M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/jobs/splitters/multi.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/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/jobs.py M 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/sharable.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/mapping.py M lib/galaxy/model/metadata.py M lib/galaxy/model/migrate/check.py M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py A lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/model/tool_shed_install/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/azure_blob.py A lib/galaxy/objectstore/cloud.py M lib/galaxy/objectstore/pithos.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/objectstore/s3_multipart_upload.py M lib/galaxy/openid/providers.py M lib/galaxy/queue_worker.py M lib/galaxy/queues.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.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/cache.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/error_reports/plugins/biostars.py M lib/galaxy/tools/error_reports/plugins/email.py M lib/galaxy/tools/error_reports/plugins/github.py M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.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/__init__.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/lint.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/locations/__init__.py M lib/galaxy/tools/locations/dockstore.py M lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/util.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py A lib/galaxy/tools/repositories.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/tools/toolbox/panel.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/tools/verify/__init__.py M lib/galaxy/tools/verify/test_data.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/util/biostar.py M lib/galaxy/util/compression_utils.py A lib/galaxy/util/facts.py M lib/galaxy/util/handlers.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/image_util.py R lib/galaxy/util/multi_byte.py M lib/galaxy/util/object_wrapper.py M lib/galaxy/util/pastescript/loadwsgi.py M lib/galaxy/util/path/__init__.py M lib/galaxy/util/permutations.py M lib/galaxy/util/properties.py A lib/galaxy/util/renamed_temporary_file.py A lib/galaxy/util/script.py M lib/galaxy/util/submodules.py M lib/galaxy/util/xml_macros.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/data_providers/phyloviz/__init__.py M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py M lib/galaxy/visualization/data_providers/registry.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/config_parser.py M lib/galaxy/visualization/plugins/registry.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/__init__.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/form_builder.py R lib/galaxy/web/framework/formbuilder.py M lib/galaxy/web/framework/helpers/__init__.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/openid_manager.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/security/__init__.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/config_manage.py M lib/galaxy/webapps/galaxy/api/annotations.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/dataset_collections.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/extended_metadata.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/folders.py M lib/galaxy/webapps/galaxy/api/forms.py M lib/galaxy/webapps/galaxy/api/histories.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/item_tags.py M lib/galaxy/webapps/galaxy/api/job_files.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/libraries.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/metrics.py M lib/galaxy/webapps/galaxy/api/page_revisions.py M lib/galaxy/webapps/galaxy/api/pages.py M lib/galaxy/webapps/galaxy/api/provenance.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/api/remote_files.py M lib/galaxy/webapps/galaxy/api/search.py 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/tools.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/async.py M lib/galaxy/webapps/galaxy/controllers/biostar.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/forms.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/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/tag.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/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 R lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/users.py M lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.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/security/__init__.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/run_request.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/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_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_dependencies/recipe/step_handler.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/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_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/repository_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/tool_dependency_util.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 R openid/yahoo.xml 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 R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R scripts/api/sequencer_configuration_create.py M scripts/build_universe_config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/data_libraries/build_lucene_index.py M scripts/db_shell.py M scripts/functional_tests.py M scripts/galaxy-main A scripts/get_uwsgi_args.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_tool_dependencies.py R scripts/manage_tools.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/summarize_timings.py M scripts/sync_reports_config.py M scripts/tool_shed/api/get_filtered_repository_revisions.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.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 R static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js R static/scripts/bundled/analysis.bundled.js.map A static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js R static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js R 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/i18n.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/masthead.js M static/scripts/layout/menu.js M static/scripts/layout/modal.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js R static/scripts/libs/bibtex.js A static/scripts/libs/bibtexParse.js M static/scripts/libs/jquery/jquery.wymeditor.js A static/scripts/libs/vue.js 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 M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/form/form-wrapper.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/hda-li-edit.js M static/scripts/mvc/history/hda-li.js M static/scripts/mvc/history/hda-model.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 A static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-preferences.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/history-view-annotated.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/history-view.js M static/scripts/mvc/history/job-dag.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/job/job-li.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/job/job-params.js 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 A static/scripts/reports/run_stats.js R static/scripts/reports_webapp/run_stats.js A static/scripts/toolshed/groups/group-detail-view.js A static/scripts/toolshed/groups/group-list-view.js A static/scripts/toolshed/groups/group-listrow-view.js A static/scripts/toolshed/groups/group-model.js A static/scripts/toolshed/toolshed.groups.js M static/scripts/ui/autocom_tagging.js M static/scripts/ui/editable-text.js M static/scripts/ui/fa-icon-button.js M static/scripts/ui/filter-control.js M static/scripts/ui/hoverhighlight.js M static/scripts/ui/loading-indicator.js M static/scripts/ui/mode-button.js M static/scripts/ui/pagination.js M static/scripts/ui/peek-column-selector.js M static/scripts/ui/popupmenu.js M static/scripts/ui/scroll-panel.js M static/scripts/ui/search-input.js M static/scripts/utils/add-logging.js M static/scripts/utils/ajax-queue.js M static/scripts/utils/async-save-text.js M static/scripts/utils/config.js M static/scripts/utils/deferred.js M static/scripts/utils/graph.js M static/scripts/utils/levenshtein.js M static/scripts/utils/localization.js M static/scripts/utils/metrics-logger.js M static/scripts/utils/natural-sort.js M static/scripts/utils/query-string-parsing.js M static/scripts/utils/uploadbox.js M static/scripts/utils/utils.js M static/scripts/viz/bbi-data-manager.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/sweepster.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/filters.js M static/scripts/viz/trackster/painters.js M static/scripts/viz/trackster/slotting.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/trackster/util.js M static/scripts/viz/visualization.js M static/scripts/viz/viz_views.js M static/style/blue/base.css M static/style/blue/library.css R templates/admin/library/grid.mako R templates/admin/library/new_library.mako M templates/admin/tool_shed_repository/common.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/repository_actions_menu.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/base.mako M templates/base/base_panels.mako R templates/common/select_template.mako R templates/common/template_common.mako M templates/display_common.mako R templates/form.mako M templates/galaxy_client_app.mako R templates/grid_base.mako R templates/grid_base_async.mako A templates/legacy/grid_base.mako A templates/legacy/grid_base_async.mako R templates/panels.mako R templates/search/index.mako M templates/show_params.mako M templates/user/index.mako M templates/user/openid_manage.mako M templates/user/register.mako M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/dataset/display.mako M templates/webapps/galaxy/dataset/tabular_chunked.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 M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/history/embed.mako M templates/webapps/galaxy/history/structure.mako M templates/webapps/galaxy/history/view.mako M templates/webapps/galaxy/history/view_multiple.mako R templates/webapps/galaxy/library/common/browse_library.mako R templates/webapps/galaxy/library/common/browse_library_opt.mako R templates/webapps/galaxy/library/common/common.mako R templates/webapps/galaxy/library/common/folder_info.mako R templates/webapps/galaxy/library/common/folder_permissions.mako R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako R templates/webapps/galaxy/library/common/ldda_edit_info.mako R templates/webapps/galaxy/library/common/ldda_info.mako R templates/webapps/galaxy/library/common/ldda_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_info.mako R templates/webapps/galaxy/library/common/library_dataset_permissions.mako R templates/webapps/galaxy/library/common/library_dataset_search_results.mako R templates/webapps/galaxy/library/common/library_info.mako R templates/webapps/galaxy/library/common/library_item_info.mako R templates/webapps/galaxy/library/common/library_permissions.mako R templates/webapps/galaxy/library/common/move_library_item.mako R templates/webapps/galaxy/library/common/new_folder.mako R templates/webapps/galaxy/library/common/upload.mako R templates/webapps/galaxy/library/grid.mako R templates/webapps/galaxy/library/index.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/user/list_users.mako M templates/webapps/galaxy/visualization/display.mako M templates/webapps/galaxy/visualization/phyloviz.mako M templates/webapps/galaxy/visualization/sweepster.mako M templates/webapps/galaxy/workflow/editor.mako R templates/webapps/reports/grid.mako M templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/1.fastqsanger M test-data/1.fastqsolexa M test-data/neostore.zip 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_tools_upload.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/api.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.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/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/config_vars.xml M test/functional/tools/create_2.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.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 M test/functional/tools/job_properties.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/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/tour_generator M test/galaxy_selenium/components.py M test/galaxy_selenium/data.py M test/galaxy_selenium/has_driver.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/galaxy_selenium/smart_components.py A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_data_manager_table_reload.py M test/integration/test_job_resubmission.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_upload_configuration_options.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 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_library_contents.py A test/selenium_tests/test_library_to_collections.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/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 A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py M test/unit/datatypes/dataproviders/test_base_dataproviders.py M test/unit/datatypes/dataproviders/test_line_dataproviders.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.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_output_checker.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_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/data_source/upload.xml M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/genomespace/genomespace_importer.py M tools/phenotype_association/senatag.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/gsummary.py M tox.ini Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into cm-datatype Commit: 9c5c7e9caa404cac1b7c1a000df5c1310775e85e https://github.com/galaxyproject/galaxy/commit/9c5c7e9caa404cac1b7c1a000df5… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- Fix Commit: 6bc2250daba23c56302e255d64ee7a8e64a4845b https://github.com/galaxyproject/galaxy/commit/6bc2250daba23c56302e255d64ee… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- to pass pylint Commit: 8e4fbe7cf35695122b77cd159b258a8e3352fa1b https://github.com/galaxyproject/galaxy/commit/8e4fbe7cf35695122b77cd159b25… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/test/infernal_model.cm Log Message: ----------- smaller cm test file Commit: a0750864a6062012a301bf612a4409659406bc54 https://github.com/galaxyproject/galaxy/commit/a0750864a6062012a301bf612a44… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- minor changes Commit: e73be6fe12f0715b275c3a75d5ce2ab66a98cb37 https://github.com/galaxyproject/galaxy/commit/e73be6fe12f0715b275c3a75d5ce… Author: Milad Miladi <miladim(a)cs.uni-freiburg.de> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- fix typo Commit: c7581f867de0b1386ded887f69ef10373cfb7e1b https://github.com/galaxyproject/galaxy/commit/c7581f867de0b1386ded887f69ef… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/msa.py A lib/galaxy/datatypes/test/infernal_model.cm Log Message: ----------- Merge pull request #4977 from mmiladi/cm-datatype add infernal-cm datatype Compare: https://github.com/galaxyproject/galaxy/compare/812f5f563047...c7581f867de0

1 0

[galaxyproject/galaxy] 823d07: Prettier upgrade to 1.10
by GitHub 10 Jan '18

10 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 823d07d41a8e0bc495a3cf31977cb7b9ae5b77a9 https://github.com/galaxyproject/galaxy/commit/823d07d41a8e0bc495a3cf31977c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/package.json M client/yarn.lock Log Message: ----------- Prettier upgrade to 1.10 Commit: e88706c282a297ef251a4cfeb8adff1d17c166f8 https://github.com/galaxyproject/galaxy/commit/e88706c282a297ef251a4cfeb8ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/package.json Log Message: ----------- Prettier now supports Vue SFCs Commit: 9cddf804fa2362e7fc13acc141a55b20c7fc98ea https://github.com/galaxyproject/galaxy/commit/9cddf804fa2362e7fc13acc141a5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue Log Message: ----------- Run client-format Commit: d79d2fa4647605d2cdc36bc8e28fb2c6a4104eca https://github.com/galaxyproject/galaxy/commit/d79d2fa4647605d2cdc36bc8e28f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js Log Message: ----------- Client build. Commit: 812f5f563047e212f10bb2718552c5be16dc6f5a https://github.com/galaxyproject/galaxy/commit/812f5f563047e212f10bb2718552… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-10 (Wed, 10 Jan 2018) Changed paths: M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue M client/galaxy/scripts/components/Message.vue M client/galaxy/scripts/components/admin/BaseGrid.vue M client/galaxy/scripts/components/admin/DataManagerGrid.vue M client/galaxy/scripts/components/admin/DataTables.vue M client/galaxy/scripts/components/admin/DataTablesGrid.vue M client/package.json M client/yarn.lock M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js Log Message: ----------- Merge pull request #5293 from dannon/prettier_1.10 Prettier 1.10 upgrade, supports Vue components now. Compare: https://github.com/galaxyproject/galaxy/compare/aa81ccf8ac13...812f5f563047

1 0