- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/usegalaxy-playbook] 9a4760: Update uniprot to 0.2, update sra_tools to 2.9.1, ...
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9a476008536d522bc34e82816ae82292682797d5 https://github.com/galaxyproject/usegalaxy-playbook/commit/9a476008536d522b… 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/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update uniprot to 0.2, update sra_tools to 2.9.1, install annotateMyIDs 3.5.0, hide CTD and DGI **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] 4c2f95: Fix hashing, AND was not the right operation
by GitHub 07 Dec '18

07 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4c2f95b1f469d9789e65c4c9be97c4e137014ece https://github.com/galaxyproject/galaxy/commit/4c2f95b1f469d9789e65c4c9be97… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Fix hashing, AND was not the right operation Commit: bddfe3889031a31ad3efd1dadd8482a6301a9ad9 https://github.com/galaxyproject/galaxy/commit/bddfe3889031a31ad3efd1dadd84… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-07 (Fri, 07 Dec 2018) Changed paths: M client/galaxy/scripts/utils/utils.js Log Message: ----------- Merge pull request #7081 from erasche/fix-hash Fix hashing, AND was not the right operation Compare: https://github.com/galaxyproject/galaxy/compare/b453f531e51c...bddfe3889031 **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] 35fd29: Fix Error display
by GitHub 06 Dec '18

06 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 35fd29062587002f70f660e4a7675bd23545fc85 https://github.com/galaxyproject/galaxy/commit/35fd29062587002f70f660e4a767… Author: jvanbraekel <29703119+jvanbraekel(a)users.noreply.github.com> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M templates/admin/tool_shed_repository/manage_repository.mako Log Message: ----------- Fix Error display The template display was broken in case of error. 'in_error_state is never defined it should be 'repository.in_error_state' instead. This was leading to some wrong field type display and not displaying the details about the error. Commit: b453f531e51c6fc91d44d777de486b31c82cf726 https://github.com/galaxyproject/galaxy/commit/b453f531e51c6fc91d44d777de48… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M templates/admin/tool_shed_repository/manage_repository.mako Log Message: ----------- Merge pull request #7080 from jvanbraekel/patch-1 Fix toolshed repository error display Compare: https://github.com/galaxyproject/galaxy/compare/16f3be66be84...b453f531e51c **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] be4369: Avoid using make for autobuild; reducing necessary...
by GitHub 06 Dec '18

06 Dec '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be43693ef05dfae85872412f198d87a31424f486 https://github.com/galaxyproject/galaxy/commit/be43693ef05dfae85872412f198d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Avoid using make for autobuild; reducing necessary dependencies out of the box. Commit: 77aec5a79dc18e224ca6246659f68a49864a46cf https://github.com/galaxyproject/galaxy/commit/77aec5a79dc18e224ca6246659f6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Standardize on spaces in common_startup.sh (tabs were mixed in here) Commit: fa408f485048ee8c7afeb96ac6c9da8dea4661f3 https://github.com/galaxyproject/galaxy/commit/fa408f485048ee8c7afeb96ac6c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-29 (Thu, 29 Nov 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- exit with error code (and appropriate message) on either build failure Commit: 66fae561b29507a69f5c32690be4791f86f5cdd7 https://github.com/galaxyproject/galaxy/commit/66fae561b29507a69f5c32690be4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-12-02 (Sun, 02 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't use pushd/popd Commit: 57459954de189cb1fd9b6ab8654c8f4700241ea2 https://github.com/galaxyproject/galaxy/commit/57459954de189cb1fd9b6ab8654c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-12-05 (Wed, 05 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7060 from dannon/no-make-for-autobuild [18.09] Eliminate dependency on make for automatic client build Commit: 16f3be66be84ac9827f4c0fa213d9ead9ba30bd2 https://github.com/galaxyproject/galaxy/commit/16f3be66be84ac9827f4c0fa213d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-12-06 (Thu, 06 Dec 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/4bf27f464216...16f3be66be84 **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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