February 2016 - galaxy-commits - lists.galaxyproject.org

[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 16 Feb '16

16 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 15 Feb '16

15 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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[galaxyproject/galaxy] fb30e2: Update SnpEffDb and SnpSiftDbNSFP vor SnpEff v4.1
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fb30e2b06103f3fbfa3dd1238c1f4e707d04b633 https://github.com/galaxyproject/galaxy/commit/fb30e2b06103f3fbfa3dd1238c1f… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-12-09 (Wed, 09 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Update SnpEffDb and SnpSiftDbNSFP vor SnpEff v4.1 Commit: acef6ab3f99e5420602ea06b77ac647599f80e5a https://github.com/galaxyproject/galaxy/commit/acef6ab3f99e5420602ea06b77ac… Author: Jim Johnson <jj(a)umn.edu> Date: 2015-12-10 (Thu, 10 Dec 2015) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Fix style errors Commit: 8fb3e461aca6f0702f45b1a5d34392893fdd2cb5 https://github.com/galaxyproject/galaxy/commit/8fb3e461aca6f0702f45b1a5d343… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1280 from jj-umn/patch-2 Update SnpEffDb and SnpSiftDbNSFP for SnpEff v4.1 Compare: https://github.com/galaxyproject/galaxy/compare/063c5ad0f87c...8fb3e461aca6

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[galaxyproject/galaxy] e0ee12: Fix problem with legacy workflows and duplicate ou...
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/release_16.01 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. Compare: https://github.com/galaxyproject/galaxy/compare/65d9ec9cab2b...ff29b2636306

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[galaxyproject/galaxy] 3e3bc1: Wrap conditional test parameters
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e3bc132d89d97fc9daac5115c63ce5c08eb0aef https://github.com/galaxyproject/galaxy/commit/3e3bc132d89d97fc9daac5115c63… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Wrap conditional test parameters Commit: 749fa90a4a67c4bd6b5b3ff24468f9b300dfb9fa https://github.com/galaxyproject/galaxy/commit/749fa90a4a67c4bd6b5b3ff24468… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Attempt to handle backward compatibility for previously unwrapped conditional test parameters Commit: 063c5ad0f87c6d7ef753608e715b64b1852745ad https://github.com/galaxyproject/galaxy/commit/063c5ad0f87c6d7ef753608e715b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py Log Message: ----------- Merge pull request #1714 from guerler/fix_conditional_wrapper_000 Wrap conditional test parameters Compare: https://github.com/galaxyproject/galaxy/compare/f8a6ee335407...063c5ad0f87c

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[galaxyproject/ansible-galaxy] 01b070: tags static setup
by GitHub 12 Feb '16

12 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 01b070656c76f3a6b425cf5c4c06d324db4e0791 https://github.com/galaxyproject/ansible-galaxy/commit/01b070656c76f3a6b425… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-11 (Thu, 11 Feb 2016) Changed paths: M tasks/main.yml Log Message: ----------- tags static setup Commit: 81856d319353f57642d3b74f3ea54a1baf9d3884 https://github.com/galaxyproject/ansible-galaxy/commit/81856d319353f57642d3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-12 (Fri, 12 Feb 2016) Changed paths: M tasks/main.yml Log Message: ----------- Merge pull request #10 from mvdbeek/add_tag tag static_setup Compare: https://github.com/galaxyproject/ansible-galaxy/compare/6209af56b96b...8185…

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