galaxy-commits December 2018

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76 discussions

[galaxyproject/galaxy] c4ab2a: Add workaround for https://github.com/travis-ci/tr...
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: c4ab2a0c6bb768fe27b48648d21ab42733133c08 https://github.com/galaxyproject/galaxy/commit/c4ab2a0c6bb768fe27b48648d21a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Add workaround for https://github.com/travis-ci/travis-ci/issues/7940 Commit: 3a1bdd0ea688948db9115a500224c5947c326e99 https://github.com/galaxyproject/galaxy/commit/3a1bdd0ea688948db9115a500224… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #7092 from martenson/boto-workaround [18.09] boto cfg workaround Compare: https://github.com/galaxyproject/galaxy/compare/57459954de18...3a1bdd0ea688 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 55bd75: Update TTS
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55bd75a7ce10d1088e75a799b5ec6e025c9a67df https://github.com/galaxyproject/usegalaxy-playbook/commit/55bd75a7ce10d108… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2de4a0: Remove legacy job handling hacks.
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2de4a0f72e5d51661318e1abeb727fdaa10f7444 https://github.com/galaxyproject/galaxy/commit/2de4a0f72e5d51661318e1abeb72… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Remove legacy job handling hacks. These were left in to let Galaxy jobs complete after version upgrades, but the plan was always to remove them eventually. Commit: 10aa953a40e171246bdd1804c74e8019da8e8200 https://github.com/galaxyproject/galaxy/commit/10aa953a40e171246bdd1804c74e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7082 from jmchilton/legacy_hacks Remove legacy job handling hacks. Compare: https://github.com/galaxyproject/galaxy/compare/11428a03b819...10aa953a40e1 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 3ae75e: Update MTS
by GitHub 11 Dec '18

11 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3ae75e93d54584e6d250f745f6d1a176cf73ba22 https://github.com/galaxyproject/usegalaxy-playbook/commit/3ae75e93d54584e6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-11 (Tue, 11 Dec 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 9bac3c: Path-aware workflows.
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9bac3c44faf51e0e4c396d7f1d3470f7aa4a588e https://github.com/galaxyproject/galaxy/commit/9bac3c44faf51e0e4c396d7f1d34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-20 (Tue, 20 Nov 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py Log Message: ----------- Path-aware workflows. - Allow workflows to be uploaded via path using the GUI and and API for admins. - Track the path and resync workflows on save (both .ga and format 2 workflows) - this will allow Planemo to leverage the Galaxy workflow editor to interactively save workflows. Commit: 11428a03b8193ff50c35d9dd7069789ca2ba6cc7 https://github.com/galaxyproject/galaxy/commit/11428a03b8193ff50c35d9dd7069… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0146_workflow_paths.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/integration/test_dockerized_jobs.py A test/integration/test_workflow_sync.py Log Message: ----------- Merge pull request #7019 from jmchilton/path-aware-workflows File-based Workflow Editor Compare: https://github.com/galaxyproject/galaxy/compare/ad42f9410204...11428a03b819 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 60fbfd: Remove older and insecure versions of SRA tools.
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 60fbfd0e4349e3b623d7dc963d03729843c415cd https://github.com/galaxyproject/usegalaxy-playbook/commit/60fbfd0e4349e3b6… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Remove older and insecure versions of SRA tools. **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 83417c: Add styled loader vue component
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 83417cab622309f9b53d8881c6946bc11e6cb3ba https://github.com/galaxyproject/galaxy/commit/83417cab622309f9b53d8881c694… Author: Ivan Kuzmin <inkuzm(a)gmail.com> Date: 2018-11-28 (Wed, 28 Nov 2018) Changed paths: A client/galaxy/scripts/components/GalaxyLoader.vue Log Message: ----------- Add styled loader vue component Commit: ad42f94102048a4c3a3695aaf88a333794aef0f7 https://github.com/galaxyproject/galaxy/commit/ad42f94102048a4c3a3695aaf88a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: A client/galaxy/scripts/components/GalaxyLoader.vue Log Message: ----------- Merge pull request #7052 from inkuzmin/dev Add styled loader vue component Compare: https://github.com/galaxyproject/galaxy/compare/1ca77d53ef2b...ad42f9410204 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c4c8af: doc: updated error parsing docs
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4c8af036fda560d5340e77d9f38782754729eb1 https://github.com/galaxyproject/galaxy/commit/c4c8af036fda560d5340e77d9f38… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-27 (Tue, 27 Nov 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- doc: updated error parsing docs see https://github.com/galaxyproject/galaxy/pull/697://github.com/galaxyproject… Commit: 1ca77d53ef2bc1067db5c3a3b5d1c36b28aeaa1b https://github.com/galaxyproject/galaxy/commit/1ca77d53ef2bc1067db5c3a3b5d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #7049 from bernt-matthias/topic/doc-errors-detection doc: updated error parsing docs Compare: https://github.com/galaxyproject/galaxy/compare/f09d7b7d9346...1ca77d53ef2b **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5c384e: Fix via refactor set_metadata so more output metad...
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5c384efb8d2ad42d6dfafa84fc09bc02d3f462e8 https://github.com/galaxyproject/galaxy/commit/5c384efb8d2ad42d6dfafa84fc09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix via refactor set_metadata so more output metadata pruned properly. Commit: f09d7b7d93463590dc8434376260248d0f3d4171 https://github.com/galaxyproject/galaxy/commit/f09d7b7d93463590dc8434376260… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #7084 from jmchilton/fix_set_metadata Fix via refactor set_metadata so more output metadata pruned properly. Compare: https://github.com/galaxyproject/galaxy/compare/e8d2b334a03c...f09d7b7d9346 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 3e57fb: Quick 'make everything private' implementation. T...
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e57fb172fbf580da04131355326681e118cc82b https://github.com/galaxyproject/galaxy/commit/3e57fb172fbf580da04131355326… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Quick 'make everything private' implementation. Takes a single history or operates on all of a user's histories. Intentionally doesn't use an API, rather a simple webcontroller endpoint, because I think we'll want to handle this with group operations and the like down the road, and will enhance existing APIs Commit: a07a1c3a566571b9b83dc7a99fae1ed0d275f020 https://github.com/galaxyproject/galaxy/commit/a07a1c3a566571b9b83dc7a99fae… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Make logic more concise, fix typo, add commentary. Commit: 43689c1f3fc8e2fc49c3d6dfc033f70fe06e4c32 https://github.com/galaxyproject/galaxy/commit/43689c1f3fc8e2fc49c3d6dfc033… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Update message to reflect all histories functionality. Commit: a3fd7084e2f02a9e9bc5383cd7f76532450774e9 https://github.com/galaxyproject/galaxy/commit/a3fd7084e2f02a9e9bc5383cd7f7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Exclude library associated datasets from history make-all-private functionality. Commit: cc53b07253538e192b8196dee300aefaf8e2fde5 https://github.com/galaxyproject/galaxy/commit/cc53b07253538e192b8196dee300… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- Update messaging to indicate library datasets are not included in the privacy pass. Commit: 5d38e558f27b2ec14088376ec1a07c3bf4b25d08 https://github.com/galaxyproject/galaxy/commit/5d38e558f27b2ec14088376ec1a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Resolve two issues from refactoring. Commit: 9b481ba9d7d34e101d54ae1ed0821f6a05b27be0 https://github.com/galaxyproject/galaxy/commit/9b481ba9d7d34e101d54ae1ed082… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-09 (Fri, 09 Nov 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Client format Commit: 4894ab9c80ae39f8b5527860618e973daee00a61 https://github.com/galaxyproject/galaxy/commit/4894ab9c80ae39f8b5527860618e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js Log Message: ----------- Add pointer to user permissions interface on finish of make datasets private Commit: e8d2b334a03c395b8c0abf54208b0e28368d0f81 https://github.com/galaxyproject/galaxy/commit/e8d2b334a03c395b8c0abf54208b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6952 from dannon/history_privacy Quick 'make all datasets private' implementation. Compare: https://github.com/galaxyproject/galaxy/compare/bddfe3889031...e8d2b334a03c **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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galaxy-commits December 2018