galaxy-commits May 2016

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[galaxyproject/galaxy] 615b0b: Fix running workflows in the background when tool ...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 615b0b444edf6648e174ff950f212c77bb4ed3f5 https://github.com/galaxyproject/galaxy/commit/615b0b444edf6648e174ff950f21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix running workflows in the background when tool bursting is enabled. Commit: 063b25f660b6d842c4193469e5c360034562b877 https://github.com/galaxyproject/galaxy/commit/063b25f660b6d842c4193469e5c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #2260 from jmchilton/fix_burst_background_workflows [16.01] Fix running workflows in the background when tool bursting is enabled. Compare: https://github.com/galaxyproject/galaxy/compare/cdea92289068...063b25f660b6

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[galaxyproject/galaxy] 14bd39: Truncate job name in DRMAA runner by default for P...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14bd39867c419ebf32f19f915b02dadd2697b57a https://github.com/galaxyproject/galaxy/commit/14bd39867c419ebf32f19f915b02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Truncate job name in DRMAA runner by default for PBSPro. We don't really have a clean way to tell if the DRMAA runner is serving to PBSPro so we make this truncation the default for the DRMAA runner but in the case of the SLURM runner we continue to not truncate. - http://dev.list.galaxyproject.org/Problem-with-DRMAA-and-Pbs-Pro-td4669338.… - http://dev.list.galaxyproject.org/If-you-need-to-use-PBS-Pro-with-Galaxy-16… Commit: 56bd4ada048ad411ca388f18e0aa2e81162a8b40 https://github.com/galaxyproject/galaxy/commit/56bd4ada048ad411ca388f18e0aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2265 from jmchilton/pbs_pro_name_fix [16.04] Truncate job name in DRMAA runner by default for PBSPro. Commit: 9fcd759e8dd244a67191d5661f71767995f67bd9 https://github.com/galaxyproject/galaxy/commit/9fcd759e8dd244a67191d5661f71… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5063384a6cbc...9fcd759e8dd2

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[galaxyproject/galaxy] af7d7d: More fixes from downstream projects.
by GitHub 03 May '16

03 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af7d7de596f89a3784c97d99e22a4386d0c46d41 https://github.com/galaxyproject/galaxy/commit/af7d7de596f89a3784c97d99e22a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/linters/general.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- More fixes from downstream projects. - Fixes a bug in lib/galaxy/tools/linters/general.py found through galaxy-lib. - Brings in docstring and import order linting fixes from the gxformat2 project (https://github.com/jmchilton/gxformat2). Commit: 5063384a6cbc9a7db9a0f252e561c522a133853c https://github.com/galaxyproject/galaxy/commit/5063384a6cbc9a7db9a0f252e561… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/tools/linters/general.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/interface.py M test/api/workflows_format_2/main.py Log Message: ----------- Merge pull request #2292 from jmchilton/more_downstream_fixes More small fixes from downstream projects. Compare: https://github.com/galaxyproject/galaxy/compare/cbf569c417e6...5063384a6cbc

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[galaxyproject/galaxy] 85a0a0: Make grunt watch (for scripts) work again, setting...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85a0a0b7bbc14c57f7759ae7b1d893da341fece5 https://github.com/galaxyproject/galaxy/commit/85a0a0b7bbc14c57f7759ae7b1d8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js Log Message: ----------- Make grunt watch (for scripts) work again, settings were being overwritten by the new watch-style command Commit: cbf569c417e6920d573a63c929c3aa0f594946c2 https://github.com/galaxyproject/galaxy/commit/cbf569c417e6920d573a63c929c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M client/grunt-tasks/scripts.js M client/grunt-tasks/style.js Log Message: ----------- Merge pull request #2296 from dannon/watch_fix Make grunt watch (for scripts) work again, settings were being overwr… Compare: https://github.com/galaxyproject/galaxy/compare/13c7143119bd...cbf569c417e6

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[galaxyproject/galaxy] b7cec9: Restore workflow slug editing javascript.
by GitHub 03 May '16

03 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7cec91bca0c36bb9fd49fa775c574c952d4cc65 https://github.com/galaxyproject/galaxy/commit/b7cec91bca0c36bb9fd49fa775c5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Restore workflow slug editing javascript. Commit: 9921fdc2b834ab28da176e9a014b0d970a944cba https://github.com/galaxyproject/galaxy/commit/9921fdc2b834ab28da176e9a014b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Remove print from workflow sharing mako. Commit: 2b6359215c8bc1a53281324ebe011c007d2c70b8 https://github.com/galaxyproject/galaxy/commit/2b6359215c8bc1a53281324ebe01… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M templates/sharing_base.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Slight refactor to eliminate duplication. Commit: 14944d810d1a8c21db245e35a3571c5b405497f7 https://github.com/galaxyproject/galaxy/commit/14944d810d1a8c21db245e35a357… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M templates/sharing_base.mako M templates/slug_editing_js.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Fix inclusion of javascripts. Commit: 13c7143119bdefa700935b7e30fdd1e1c0f01298 https://github.com/galaxyproject/galaxy/commit/13c7143119bdefa700935b7e30fd… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M templates/sharing_base.mako A templates/slug_editing_js.mako M templates/webapps/galaxy/workflow/sharing.mako Log Message: ----------- Merge pull request #2293 from dannon/workflow_sharing_tweaks Workflow sharing slug edit fix. Compare: https://github.com/galaxyproject/galaxy/compare/786a26c473f3...13c7143119bd

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[galaxyproject/galaxy] 14bd39: Truncate job name in DRMAA runner by default for P...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 14bd39867c419ebf32f19f915b02dadd2697b57a https://github.com/galaxyproject/galaxy/commit/14bd39867c419ebf32f19f915b02… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-28 (Thu, 28 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Truncate job name in DRMAA runner by default for PBSPro. We don't really have a clean way to tell if the DRMAA runner is serving to PBSPro so we make this truncation the default for the DRMAA runner but in the case of the SLURM runner we continue to not truncate. - http://dev.list.galaxyproject.org/Problem-with-DRMAA-and-Pbs-Pro-td4669338.… - http://dev.list.galaxyproject.org/If-you-need-to-use-PBS-Pro-with-Galaxy-16… Commit: 56bd4ada048ad411ca388f18e0aa2e81162a8b40 https://github.com/galaxyproject/galaxy/commit/56bd4ada048ad411ca388f18e0aa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #2265 from jmchilton/pbs_pro_name_fix [16.04] Truncate job name in DRMAA runner by default for PBSPro. Compare: https://github.com/galaxyproject/galaxy/compare/d282ed9ce3e8...56bd4ada048a

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[galaxyproject/galaxy] 1cc914: Minor documentation spellos.
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1cc91412a7012e0e6e9bf97da570e7138d9e2fac https://github.com/galaxyproject/galaxy/commit/1cc91412a7012e0e6e9bf97da570… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/lint.py Log Message: ----------- Minor documentation spellos. Commit: 786a26c473f3d11e1b8d6c455b253050df0bf29f https://github.com/galaxyproject/galaxy/commit/786a26c473f3d11e1b8d6c455b25… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/lint.py Log Message: ----------- Merge pull request #2289 from dannon/lint_16.04 Minor documentation spellos. Compare: https://github.com/galaxyproject/galaxy/compare/5ff1693dd4da...786a26c473f3

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[galaxyproject/galaxy] 364f38: Enhance library functions for tools.
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 364f383ca8a3448e3cffa436acc0bf58d7895274 https://github.com/galaxyproject/galaxy/commit/364f383ca8a3448e3cffa436acc0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Enhance library functions for tools. - Enhance lint and loaders to be able to handle tool parser objects instead of just raw XML. This will allow non-Galaxy-XML tool linting (e.g. CWL) and allow linters to use higher-level abstraction. - Rework CWL tool loading to allow more fine-grain loading. - Replace tol-level XML linter with a "general" linter that parses attributes using the ToolSource abstraction. - Small updates to linting for recent additions to tool framework. - More docstring usage and improved import order. - Fixes discovered through planemo for "finding" non-XML tools. Commit: e477504a8e371443da49f64139c27d037fa3b1d7 https://github.com/galaxyproject/galaxy/commit/e477504a8e371443da49f64139c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Misc fixes to #2279 Commit: 49a4f352d148d126c3f428763288874d6d55cf37 https://github.com/galaxyproject/galaxy/commit/49a4f352d148d126c3f428763288… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Merge pull request #47 from dannon/lint_16.04 Misc fixes to #2279 Commit: 5ff1693dd4da53550401ae1b1f8b40338bd79706 https://github.com/galaxyproject/galaxy/commit/5ff1693dd4da53550401ae1b1f8b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py A lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/__init__.py M lib/galaxy/tools/linters/citations.py M lib/galaxy/tools/linters/command.py A lib/galaxy/tools/linters/general.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py R lib/galaxy/tools/linters/top_level.py M lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/xml.py Log Message: ----------- Merge pull request #2279 from jmchilton/lint_16.04 Enhance library functions for tools. Compare: https://github.com/galaxyproject/galaxy/compare/2df8edf6b149...5ff1693dd4da

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[galaxyproject/galaxy] 49bb0d: Shift asbool handling in datatypes api so that an ...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 49bb0d69182b71ae74934353fbf497fb25dafd73 https://github.com/galaxyproject/galaxy/commit/49bb0d69182b71ae74934353fbf4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Shift asbool handling in datatypes api so that an appropriate error message is now returned for requests like ?extension_only=LDKFJSLKDFJKLJ Commit: 2df8edf6b14978b0e1ae520e6a8aef0155bc2bde https://github.com/galaxyproject/galaxy/commit/2df8edf6b14978b0e1ae520e6a8a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Merge pull request #2286 from dannon/datatypes_api_exception_handling Shift asbool handling in datatypes api so that an appropriate error m… Compare: https://github.com/galaxyproject/galaxy/compare/36763abe1201...2df8edf6b149

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[galaxyproject/galaxy] 31583c: fix searching on hyphenated strings; index and sea...
by GitHub 02 May '16

02 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31583c31500561525f1399f6ed4d52266a553f63 https://github.com/galaxyproject/galaxy/commit/31583c31500561525f1399f6ed4d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-29 (Fri, 29 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- fix searching on hyphenated strings; index and search on tool id stub (tool id stub is a part of a long tool id that does not have the TS part nor the version i.e. it has owner+repo+toolname) also introduce config boost for labels and id stubs Commit: 36763abe1201ff2e1f84418569c2915973df76b1 https://github.com/galaxyproject/galaxy/commit/36763abe1201ff2e1f84418569c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Merge pull request #2273 from martenson/adjust-toolbox-search improvements to toolbox search Compare: https://github.com/galaxyproject/galaxy/compare/5cd6b47d6890...36763abe1201

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galaxy-commits May 2016