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

[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Commit: 8d512c98e237b20235bddbd74424b3c0e09c0f1c https://github.com/galaxyproject/galaxy/commit/8d512c98e237b20235bddbd74424… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 0210fb31b67635fe134b3c79e7abe3fb353c822e https://github.com/galaxyproject/galaxy/commit/0210fb31b67635fe134b3c79e7ab… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/3af38018a57c...0210fb31b676

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Commit: 8d512c98e237b20235bddbd74424b3c0e09c0f1c https://github.com/galaxyproject/galaxy/commit/8d512c98e237b20235bddbd74424… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/a13117fdf570...8d512c98e237

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Commit: bcfcd8184f297abc9f2e90fbf7504be08725600e https://github.com/galaxyproject/galaxy/commit/bcfcd8184f297abc9f2e90fbf750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/f8cf6f834bd9...bcfcd8184f29

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[galaxyproject/infrastructure-playbook] c79aa6: Missed one
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c79aa649300f70fec8462928c11d314b9603d31f https://github.com/galaxyproject/infrastructure-playbook/commit/c79aa649300… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml Log Message: ----------- Missed one

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[galaxyproject/infrastructure-playbook] 58c9e2: Create Galaxy directories
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 58c9e218f4e1bfeefe7188bbe9a6b12b0111fd49 https://github.com/galaxyproject/infrastructure-playbook/commit/58c9e218f4e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml A taccenv/group_vars/maingalaxyservers.yml A taccenv/group_vars/testgalaxyservers.yml Log Message: ----------- Create Galaxy directories

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[galaxyproject/galaxy] 43320a: Conda explicitly checks for .sh in the command as ...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 43320aa8d1443c3ca3b95185544ae27817ba71b6 https://github.com/galaxyproject/galaxy/commit/43320aa8d1443c3ca3b95185544a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Conda explicitly checks for .sh in the command as a part of it's logic to figure out that the shell is sh or bash compatible. Commit: 752df7f82b129d9a6f827f2421ffdb135ee111bc https://github.com/galaxyproject/galaxy/commit/752df7f82b129d9a6f827f2421ff… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #2788 from dannon/backport_condainstall [16.04] Conda explicitly checks for .sh in the command as a part of it's logi… Compare: https://github.com/galaxyproject/galaxy/compare/ceeef39edb55...752df7f82b12

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[galaxyproject/usegalaxy-playbook] 2fd86c: Update Test
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2fd86c6db792153e0a26ac74abb46f08ab13dc88 https://github.com/galaxyproject/usegalaxy-playbook/commit/2fd86c6db792153e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M stage/galaxy_version.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Test Commit: dcfc8bcc28e3dd46d45c984c608c9371574e2bd0 https://github.com/galaxyproject/usegalaxy-playbook/commit/dcfc8bcc28e3dd46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M production/galaxy_version.yml M production/group_vars/galaxyservers.yml Log Message: ----------- Update Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c7c0a524a778...…

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[galaxyproject/galaxy] 85aaa2: Make conda install and resolver status more robust
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85aaa23785ff10337b40d9a5f4316e8a4683668d https://github.com/galaxyproject/galaxy/commit/85aaa23785ff10337b40d9a5f431… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Make conda install and resolver status more robust We disable the conda resolver if conda_exec is not found and we are unable to install conda. Skip installing conda if it won't be used (because conda exec is outside of conda_prefix). Install conda if conda_prefix is an empty directory. Commit: fdc43a1448453afa1e65ae43f20b71865762882d https://github.com/galaxyproject/galaxy/commit/fdc43a1448453afa1e65ae43f20b… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Rephrase conda options and explain conda_prefix, add current length limitation Commit: 0cc10d184dfb949130fefedfe12258241f4982c9 https://github.com/galaxyproject/galaxy/commit/0cc10d184dfb949130fefedfe122… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Move can_install_conda and is_conda_installed into CondaContext Commit: 30a14e3c392395805453f15d35b9d9c0b76a65ee https://github.com/galaxyproject/galaxy/commit/30a14e3c392395805453f15d35b9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Raise a more specific exception Commit: 40f8589c3830af3c4ca69ebcd394d9bf5a53e65b https://github.com/galaxyproject/galaxy/commit/40f8589c3830af3c4ca69ebcd394… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2789 from mvdbeek/is_conda_installed Make conda install and resolver status more robust Commit: c3c97cef1e1fb9aeb03e2b12e0619172f245b2f0 https://github.com/galaxyproject/galaxy/commit/c3c97cef1e1fb9aeb03e2b12e061… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Do not start tool conf watchdog threads until postfork Commit: 59e88fa6f7471e59526c183bc9624f1158ac8160 https://github.com/galaxyproject/galaxy/commit/59e88fa6f7471e59526c183bc962… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Do not instantiate the raven (sentry) client until uWSGI postfork Commit: c431d8c06cc44dee60d986a230007dff9450a08c https://github.com/galaxyproject/galaxy/commit/c431d8c06cc44dee60d986a23000… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix import linting error Commit: a13117fdf5708b2060405e414e26f7c114ca0a42 https://github.com/galaxyproject/galaxy/commit/a13117fdf5708b2060405e414e26… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #2792 from natefoo/uwsgi-fork-raven [16.07] Do not instantiate the raven (sentry) client or tool conf watchdog threads until uWSGI postfork Commit: 3af38018a57c7e9171e06f589c0200da1a9e8fc3 https://github.com/galaxyproject/galaxy/commit/3af38018a57c7e9171e06f589c02… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b62d0073919a...3af38018a57c

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[galaxyproject/galaxy] ea72ca: Remove legacy select builder and form collector fo...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ea72cae91094502af16224c25ddc9487ac2b6eba https://github.com/galaxyproject/galaxy/commit/ea72cae91094502af16224c25ddc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove legacy select builder and form collector for post actions Commit: f0929a9f512dece09167108489e5789452fc76d9 https://github.com/galaxyproject/galaxy/commit/f0929a9f512dece09167108489e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Remove shared form builder function for legacy post action forms Commit: b62d0073919ac0cb041db6cc740db418ec73be42 https://github.com/galaxyproject/galaxy/commit/b62d0073919ac0cb041db6cc740d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #2799 from guerler/strip_action_forms Strip legacy post action forms from backend Compare: https://github.com/galaxyproject/galaxy/compare/7854047251f9...b62d0073919a

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[galaxyproject/galaxy] c3c97c: Do not start tool conf watchdog threads until post...
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c3c97cef1e1fb9aeb03e2b12e0619172f245b2f0 https://github.com/galaxyproject/galaxy/commit/c3c97cef1e1fb9aeb03e2b12e061… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/tools/toolbox/watcher.py Log Message: ----------- Do not start tool conf watchdog threads until postfork Commit: 59e88fa6f7471e59526c183bc9624f1158ac8160 https://github.com/galaxyproject/galaxy/commit/59e88fa6f7471e59526c183bc962… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Do not instantiate the raven (sentry) client until uWSGI postfork Commit: c431d8c06cc44dee60d986a230007dff9450a08c https://github.com/galaxyproject/galaxy/commit/c431d8c06cc44dee60d986a23000… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix import linting error Commit: a13117fdf5708b2060405e414e26f7c114ca0a42 https://github.com/galaxyproject/galaxy/commit/a13117fdf5708b2060405e414e26… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #2792 from natefoo/uwsgi-fork-raven [16.07] Do not instantiate the raven (sentry) client or tool conf watchdog threads until uWSGI postfork Compare: https://github.com/galaxyproject/galaxy/compare/40f8589c3830...a13117fdf570

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