February 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 317259: Fix conda resolver when conda_auto_init = True and...
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 31725972ef9342145effa6ad24d912022afb278c https://github.com/galaxyproject/galaxy/commit/31725972ef9342145effa6ad24d9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix conda resolver when conda_auto_init = True and install = False Conda dependencies were being prematurely installed during installation of repositories from the ToolShed (at the point where we are just trying to list already installed dependencies). Commit: 0ce7f6897fe7a037ae9ff9a79c082c56fec0e929 https://github.com/galaxyproject/galaxy/commit/0ce7f6897fe7a037ae9ff9a79c08… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- add comments from @mvdbeek Commit: 961efb4d9af9ea17fbd0f80b7f07158f2cb971ad https://github.com/galaxyproject/galaxy/commit/961efb4d9af9ea17fbd0f80b7f07… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3536 from blankenberg/17.01-conda-fix [17.01] Fix conda resolver when conda_auto_install = True and install = False Compare: https://github.com/galaxyproject/galaxy/compare/f1062afa55c4...961efb4d9af9

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[galaxyproject/galaxy] c2e029: Fix output tests for checksum example tools.
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c2e0295e0232d059de9ceb87081eec74dc3188f1 https://github.com/galaxyproject/galaxy/commit/c2e0295e0232d059de9ceb87081e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/functional/tools/checksum.xml M test/functional/tools/md5sum.xml Log Message: ----------- Fix output tests for checksum example tools. Fixes #3544 - thanks to @jvolkening for the heads up. Commit: de509a81a1c019f9f2036783f8b958ee9898f321 https://github.com/galaxyproject/galaxy/commit/de509a81a1c019f9f2036783f8b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/functional/tools/checksum.xml M test/functional/tools/md5sum.xml Log Message: ----------- Merge pull request #3545 from jmchilton/fix_checksum Fix output tests for checksum example tools. Compare: https://github.com/galaxyproject/galaxy/compare/3681dae83808...de509a81a1c0

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[galaxyproject/usegalaxy-playbook] 6af39a: Update ansible-common-roles submodule
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6af39a55ffde93c80f69fdc136c3b640d4fa2cd4 https://github.com/galaxyproject/usegalaxy-playbook/commit/6af39a55ffde93c8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M common_roles Log Message: ----------- Update ansible-common-roles submodule

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[galaxyproject/usegalaxy-playbook] b65bef: Update Main
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b65bef9dc17124285c8417e0bdb1914693d0311a https://github.com/galaxyproject/usegalaxy-playbook/commit/b65bef9dc1712428… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] ddcbd8: add jenkins documentation tasks for release issue
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ddcbd8ba02b628defc3c1593e402769621798ac4 https://github.com/galaxyproject/galaxy/commit/ddcbd8ba02b628defc3c1593e402… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-31 (Tue, 31 Jan 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- add jenkins documentation tasks for release issue Commit: 3681dae83808e7a683f3d717151e10002b0b4b58 https://github.com/galaxyproject/galaxy/commit/3681dae83808e7a683f3d717151e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #3523 from martenson/tweak-bootstrap-template add jenkins documentation tasks to the release issue Compare: https://github.com/galaxyproject/galaxy/compare/c5da4f0f001d...3681dae83808

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[galaxyproject/galaxy] c60233: Fix for rerunning a job when the tool does not exi...
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: c602336cc82fe60c54d10834c26fb8b0eafe81b0 https://github.com/galaxyproject/galaxy/commit/c602336cc82fe60c54d10834c26f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Fix for rerunning a job when the tool does not exist. Commit: f1062afa55c486a0b35418bf7e7e988136c78cb6 https://github.com/galaxyproject/galaxy/commit/f1062afa55c486a0b35418bf7e7e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Merge pull request #3538 from blankenberg/fix-rerun-no-tool [17.01] Fix for rerunning a job when the tool does not exist. Compare: https://github.com/galaxyproject/galaxy/compare/2322bc1ff59e...f1062afa55c4

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[galaxyproject/galaxy] 840c3b: Fix integration test for default Conda mapping.
by GitHub 02 Feb '17

02 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 840c3b0fd846ea5fb58fb34378717aeadea7e81a https://github.com/galaxyproject/galaxy/commit/840c3b0fd846ea5fb58fb3437871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Fix integration test for default Conda mapping. It worked locally simply because I had R already installed on my system globally. Commit: 2322bc1ff59e85fb4f9db281d04b96e124dd73aa https://github.com/galaxyproject/galaxy/commit/2322bc1ff59e85fb4f9db281d04b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-02-02 (Thu, 02 Feb 2017) Changed paths: M test/integration/test_resolvers.py Log Message: ----------- Merge pull request #3541 from jmchilton/backport_3508 [17.01] Fix integration test for default Conda mapping. Compare: https://github.com/galaxyproject/galaxy/compare/da0affd45d4f...2322bc1ff59e

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[galaxyproject/galaxy] a7cc18: Fix tools that use Galaxy sequence utilities for #...
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: a7cc18d616a2fe020d1946eac91ab248f9a1c995 https://github.com/galaxyproject/galaxy/commit/a7cc18d616a2fe020d1946eac91a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tools that use Galaxy sequence utilities for #3364. Thanks to @peterjc for reporting and @martenson for grepping. xref #minor #3364 Commit: da0affd45d4fb5479d0e0adcc4efa147bee41e63 https://github.com/galaxyproject/galaxy/commit/da0affd45d4fb5479d0e0adcc4ef… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3542 from jmchilton/more_python_preservation [17.01] Fix tools that use Galaxy sequence utilities for #3364. Compare: https://github.com/galaxyproject/galaxy/compare/bb15a431f006...da0affd45d4f

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[galaxyproject/galaxy] da7fed: Fix wiggle to wiggle2simple1 for Python path chang...
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: da7fed47445d8d1483eb456f32af19a0b0ff5412 https://github.com/galaxyproject/galaxy/commit/da7fed47445d8d1483eb456f32af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix wiggle to wiggle2simple1 for Python path changes in #3364. Fixes #3539. #minor Commit: bb15a431f006dfbe0d9777529300b8e1981fc988 https://github.com/galaxyproject/galaxy/commit/bb15a431f006dfbe0d9777529300… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3540 from jmchilton/wiggle_fix_1701 [17.01] Fix wiggle to wiggle2simple1 for Python path changes in #3364. Compare: https://github.com/galaxyproject/galaxy/compare/3858528d90c1...bb15a431f006

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[galaxyproject/galaxy] a121b8: Only read 6 bytes.
by GitHub 01 Feb '17

01 Feb '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: a121b889ef584086c96c6b9230198b3e2a04d6f6 https://github.com/galaxyproject/galaxy/commit/a121b889ef584086c96c6b923019… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Only read 6 bytes. Fixes #3529 Commit: 3858528d90c1380ae33c7e6087ee3ee1a9bb85f9 https://github.com/galaxyproject/galaxy/commit/3858528d90c1380ae33c7e6087ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-02-01 (Wed, 01 Feb 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3537 from jmchilton/backport_genbank_fix [17.01] Backport of fix unbounded readline in genbank datatype Compare: https://github.com/galaxyproject/galaxy/compare/9dc1bbd3bc46...3858528d90c1

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