- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c56635: Make api/tools return tool_shed_repository informa...
by GitHub 18 Feb '16

18 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c56635ad2883df92575c85a5946726037ceef600 https://github.com/galaxyproject/galaxy/commit/c56635ad2883df92575c85a59467… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Make api/tools return tool_shed_repository information. Commit: f5277a654a048869d213f4941198ef43c03a46b6 https://github.com/galaxyproject/galaxy/commit/f5277a654a048869d213f4941198… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1752 from mvdbeek/return_tsr_info_on_tools_api Make api/tools return tool_shed_repository information. Compare: https://github.com/galaxyproject/galaxy/compare/e3b1fc1bef99...f5277a654a04

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[galaxyproject/galaxy] 80f4a5: [PROCEDURES] Drop Ross from the committers group.
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80f4a5eaed2ec17e5ef97dc800707ea56a60d6dd https://github.com/galaxyproject/galaxy/commit/80f4a5eaed2ec17e5ef97dc80070… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- [PROCEDURES] Drop Ross from the committers group. Ross Lazarus has done a lot for Galaxy for a long time and has been a fantastic presence in the community. He is now retired and has no intention of touching the code or reviewing pull requests so I think it is best to remove him from the committers list. I have contacted him to confirm this and he has no problem with his removal from this group. Just to reiterate, this isn't a condemnation of any kind, from the organization policies - "Periodically, active members may review this group and request inactive members are removed - this should not be interpreted as a condemnation of these inactive members but merely as a reflection of a desire to keep this group focused enough to remain effective." Commit: e3b1fc1bef99bca281e6a86f927b44bbfa7fdaae https://github.com/galaxyproject/galaxy/commit/e3b1fc1bef99bca281e6a86f927b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1698 from jmchilton/ross [PROCEDURES] Drop Ross from the committers group. Compare: https://github.com/galaxyproject/galaxy/compare/b3296526da94...e3b1fc1bef99

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[galaxyproject/galaxy] b2da13: [PROCEDURES] Add Marius van den Beek to Galaxy com...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b2da133e07c971afd35963c50b9b36eb5b24a358 https://github.com/galaxyproject/galaxy/commit/b2da133e07c971afd35963c50b9b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-08 (Mon, 08 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- [PROCEDURES] Add Marius van den Beek to Galaxy committer group. Marius has been an indispensable member of the Galaxy community for a while - his contributions to tools, planemo, and ansible roles have been signficant and invaluable. However over the last several months he has taken a very active role on the Galaxy central code base itself. He has worked through a number of very intricate bugs to tool shed, tooling, and workflow code - consistently providing high quality and important bug fixes. Beyond that he has made signficant enhancements to the testing of Galaxy and workflow available to tool developers leveraging local tool sheds. He also is very active in the review of issues and pull requests, perhaps the most important role of Galaxy committer group members. Commit: b3296526da94cee8ffd1acdf3186548d967f075f https://github.com/galaxyproject/galaxy/commit/b3296526da94cee8ffd1acdf3186… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1699 from jmchilton/mvdbeek [PROCEDURES] Add Marius van den Beek to Galaxy committer group. Compare: https://github.com/galaxyproject/galaxy/compare/8e5aa4ac6774...b3296526da94

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[galaxyproject/infrastructure-playbook] 1bd157: Change access lists for orval
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1bd1570dcd2376995d29468e5c67ea630ec8ef09 https://github.com/galaxyproject/infrastructure-playbook/commit/1bd1570dcd2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml Log Message: ----------- Change access lists for orval

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[galaxyproject/galaxy] 37b98b: Load whitelist regardless of whether the setting i...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 37b98b773ea378bdd4a7845d60f589f7454f2291 https://github.com/galaxyproject/galaxy/commit/37b98b773ea378bdd4a7845d60f5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Load whitelist regardless of whether the setting is explicit in config. This is a sensible enough default, and requiring the option to be set in galaxy.ini is cumbersome and unnecessary since it's admin-only functionality. Commit: aabc916ed20ac7f25174ce4d552b735253697081 https://github.com/galaxyproject/galaxy/commit/aabc916ed20ac7f25174ce4d552b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1749 from dannon/whitelist_loading Load whitelist regardless of whether the setting is explicit in config. Compare: https://github.com/galaxyproject/galaxy/compare/39ec09df4806...aabc916ed20a

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[galaxyproject/galaxy] e0ee12: Fix problem with legacy workflows and duplicate ou...
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e0ee1203c6fc176ffb56ecd717540cc6b2f0b0e7 https://github.com/galaxyproject/galaxy/commit/e0ee1203c6fc176ffb56ecd71754… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Fix problem with legacy workflows and duplicate output labels. Fixes #1704 - many thanks to @tzk and @mvdbeek. Commit: ff29b263630614b96c617eb9468afcec9d04d72f https://github.com/galaxyproject/galaxy/commit/ff29b263630614b96c617eb9468a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1718 from jmchilton/workflow_fixes [16.01] Fix problem with legacy workflows and duplicate output labels. Commit: 75a3797d0fa03fc80240326e6b7fdae40ee5d658 https://github.com/galaxyproject/galaxy/commit/75a3797d0fa03fc80240326e6b7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Also fix legacy export. Commit: 00b739fc1451d7a529913ab626358bd968e75ee3 https://github.com/galaxyproject/galaxy/commit/00b739fc1451d7a529913ab62635… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1733 from mvdbeek/legacy_export [16.01] Also check for unique outputs on legacy workflow export Commit: 4a566b6db8ac69bf5f5619e9a9aa2640ce3bd9af https://github.com/galaxyproject/galaxy/commit/4a566b6db8ac69bf5f5619e9a9aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved debug message in workflow scheduling. Commit: 39ec09df48060e4e384d7af2669a6fe074b6d71a https://github.com/galaxyproject/galaxy/commit/39ec09df48060e4e384d7af2669a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1741 from jmchilton/workflow_schedule_fixes [16.01] Improved debug message in workflow scheduling. Commit: 8e5aa4ac6774df0426d6f0ba458222dd061177e9 https://github.com/galaxyproject/galaxy/commit/8e5aa4ac6774df0426d6f0ba4582… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-17 (Wed, 17 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3ee0594c692f...8e5aa4ac6774

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[galaxyproject/usegalaxy-playbook] f167a3: Bump Naive Variant Caller on Main to 64GB
by GitHub 17 Feb '16

17 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f167a34d0b4ff9105e76a5ab0c1ff0f07165ff58 https://github.com/galaxyproject/usegalaxy-playbook/commit/f167a34d0b4ff910… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Bump Naive Variant Caller on Main to 64GB

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[galaxyproject/galaxy] 4a566b: Improved debug message in workflow scheduling.
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4a566b6db8ac69bf5f5619e9a9aa2640ce3bd9af https://github.com/galaxyproject/galaxy/commit/4a566b6db8ac69bf5f5619e9a9aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved debug message in workflow scheduling. Commit: 39ec09df48060e4e384d7af2669a6fe074b6d71a https://github.com/galaxyproject/galaxy/commit/39ec09df48060e4e384d7af2669a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #1741 from jmchilton/workflow_schedule_fixes [16.01] Improved debug message in workflow scheduling. Compare: https://github.com/galaxyproject/galaxy/compare/00b739fc1451...39ec09df4806

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[galaxyproject/galaxy] fad3e1: workaround for error message in case original tool...
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fad3e1fd73adad84ae9b723534ed16f95afcdfe3 https://github.com/galaxyproject/galaxy/commit/fad3e1fd73adad84ae9b723534ed… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 3ee0594c692faac542ffa58f4339d79b9b8aefbd https://github.com/galaxyproject/galaxy/commit/3ee0594c692faac542ffa58f4339… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1738 from mvdbeek/workflow_from_different_toolshed_fix workaround for error message on tool lookup in case original toolshed had been disabled Compare: https://github.com/galaxyproject/galaxy/compare/8fb3e461aca6...3ee0594c692f

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[galaxyproject/galaxy] 75a379: Also fix legacy export.
by GitHub 16 Feb '16

16 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 75a3797d0fa03fc80240326e6b7fdae40ee5d658 https://github.com/galaxyproject/galaxy/commit/75a3797d0fa03fc80240326e6b7f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Also fix legacy export. Commit: 00b739fc1451d7a529913ab626358bd968e75ee3 https://github.com/galaxyproject/galaxy/commit/00b739fc1451d7a529913ab62635… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1733 from mvdbeek/legacy_export [16.01] Also check for unique outputs on legacy workflow export Compare: https://github.com/galaxyproject/galaxy/compare/ff29b2636306...00b739fc1451

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