- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 71a877: Check job_directory is set or not
by GitHub 16 Aug '16

16 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 71a877ade6a68f3d0abf7df53031bb93383563c6 https://github.com/galaxyproject/galaxy/commit/71a877ade6a68f3d0abf7df53031… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Check job_directory is set or not Commit: 54bda33fd382db1d0fb5341a1c95d5822b34f81d https://github.com/galaxyproject/galaxy/commit/54bda33fd382db1d0fb5341a1c95… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Add missing comma Commit: 7854047251f991ee093fea4c35e001614138ba39 https://github.com/galaxyproject/galaxy/commit/7854047251f991ee093fea4c35e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-16 (Tue, 16 Aug 2016) Changed paths: M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2763 from manabuishii/job_directory Check job_directory is set or not Compare: https://github.com/galaxyproject/galaxy/compare/f1f20d9eb0bf...7854047251f9

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[galaxyproject/galaxy] 690d83: HDT format added and turtle sniffer improved
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 690d835626ede43a096759a0bcb5ff749397037f https://github.com/galaxyproject/galaxy/commit/690d835626ede43a096759a0bcb5… Author: Jasper Koehorst <jasperkoehorst(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/triples.py Log Message: ----------- HDT format added and turtle sniffer improved Commit: d072a6be732a6846088e3f77333b300e5aedd008 https://github.com/galaxyproject/galaxy/commit/d072a6be732a6846088e3f77333b… Author: Jasper Koehorst <jasperkoehorst(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- edam format Commit: 6792645ffe414754500ac2746e5465dc48485ea1 https://github.com/galaxyproject/galaxy/commit/6792645ffe414754500ac2746e54… Author: Jasper <jasperkoehorst(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- changed to test first 4 characters Commit: f1f20d9eb0bf96ee3ca2c1fcf19b68712c901c1f https://github.com/galaxyproject/galaxy/commit/f1f20d9eb0bf96ee3ca2c1fcf19b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/triples.py Log Message: ----------- Merge pull request #2787 from jjkoehorst/dev HDT format added and turtle sniffer improved Compare: https://github.com/galaxyproject/galaxy/compare/62d69be1565d...f1f20d9eb0bf

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[galaxyproject/galaxy] 85aaa2: Make conda install and resolver status more robust
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/release_16.07 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 Compare: https://github.com/galaxyproject/galaxy/compare/d87fbdd5b80b...40f8589c3830

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[galaxyproject/galaxy] af533a: Create a uWSGI postfork function registry. Also, s...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af533a7a6ff0106185350466b31153e40c394389 https://github.com/galaxyproject/galaxy/commit/af533a7a6ff0106185350466b311… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Create a uWSGI postfork function registry. Also, start the tool conf watcher thread post-fork. Commit: 7ebf7e57063624758eaea62756126fd556cfa989 https://github.com/galaxyproject/galaxy/commit/7ebf7e57063624758eaea6275612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Force update repository manager to launch postfork. Commit: 7c5cadbe7dc81423821d0809451ad5e2fdb8d53a https://github.com/galaxyproject/galaxy/commit/7c5cadbe7dc81423821d0809451a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future. Commit: fb6f3c9c698a14d9f67fe6262e16c65ddc78477e https://github.com/galaxyproject/galaxy/commit/fb6f3c9c698a14d9f67fe6262e16… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/style/less/library.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- separate styles of new and old libs fixing various ui bugs Commit: 0719d83837aacf45b200709cb7b243badca87488 https://github.com/galaxyproject/galaxy/commit/0719d83837aacf45b200709cb7b2… Author: Carl Eberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M client/galaxy/style/less/library.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #2780 from martenson/lib-style-fix [16.07] separate styles of new and old libraries fixing various ui bugs Commit: efbd8f2d9fd68dac5039ae21dedb1be1e5cd23bc https://github.com/galaxyproject/galaxy/commit/efbd8f2d9fd68dac5039ae21dedb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Separates the decorator from the injected uwsgi package to fix 'process_is_uwsgi' logic. Commit: 2f0c4562ae3314caa58c7ff1b87ecbd34c485966 https://github.com/galaxyproject/galaxy/commit/2f0c4562ae3314caa58c7ff1b87e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #4 from dannon/uwsgi-fork Force update repository manager to launch postfork. Commit: 699e955d7f3bde9744d6a6cc0b0d2ec73eaa03bd https://github.com/galaxyproject/galaxy/commit/699e955d7f3bde9744d6a6cc0b0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available. Commit: be7c5bce1d93dfe5ab28f3176488f32400d7e415 https://github.com/galaxyproject/galaxy/commit/be7c5bce1d93dfe5ab28f3176488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Words. Commit: 6ca6f9019ee034550d8da1eedfa66619bce0e584 https://github.com/galaxyproject/galaxy/commit/6ca6f9019ee034550d8da1eedfa6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge pull request #5 from dannon/uwsgi-fork Add a warning when it is detected that a process is uwsgi based but u… Commit: d87fbdd5b80b110d3f0a0f8805b63eb2246a28cb https://github.com/galaxyproject/galaxy/commit/d87fbdd5b80b110d3f0a0f8805b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #2774 from natefoo/uwsgi-fork [16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork Commit: 62d69be1565d8d854fe8bd0a289732ec9e12001c https://github.com/galaxyproject/galaxy/commit/62d69be1565d8d854fe8bd0a2897… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M client/galaxy/style/less/library.less M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d20828b685e5...62d69be1565d

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[galaxyproject/galaxy] af533a: Create a uWSGI postfork function registry. Also, s...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: af533a7a6ff0106185350466b31153e40c394389 https://github.com/galaxyproject/galaxy/commit/af533a7a6ff0106185350466b311… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Create a uWSGI postfork function registry. Also, start the tool conf watcher thread post-fork. Commit: 7ebf7e57063624758eaea62756126fd556cfa989 https://github.com/galaxyproject/galaxy/commit/7ebf7e57063624758eaea6275612… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Force update repository manager to launch postfork. Commit: 7c5cadbe7dc81423821d0809451ad5e2fdb8d53a https://github.com/galaxyproject/galaxy/commit/7c5cadbe7dc81423821d0809451a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add debugging to indicate running threads just prior to prefork, to make finding and fixing of these easier in the future. Commit: efbd8f2d9fd68dac5039ae21dedb1be1e5cd23bc https://github.com/galaxyproject/galaxy/commit/efbd8f2d9fd68dac5039ae21dedb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Separates the decorator from the injected uwsgi package to fix 'process_is_uwsgi' logic. Commit: 2f0c4562ae3314caa58c7ff1b87ecbd34c485966 https://github.com/galaxyproject/galaxy/commit/2f0c4562ae3314caa58c7ff1b87e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #4 from dannon/uwsgi-fork Force update repository manager to launch postfork. Commit: 699e955d7f3bde9744d6a6cc0b0d2ec73eaa03bd https://github.com/galaxyproject/galaxy/commit/699e955d7f3bde9744d6a6cc0b0d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Add a warning when it is detected that a process is uwsgi based but uwsgidecorators is not available. Commit: be7c5bce1d93dfe5ab28f3176488f32400d7e415 https://github.com/galaxyproject/galaxy/commit/be7c5bce1d93dfe5ab28f3176488… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Words. Commit: 6ca6f9019ee034550d8da1eedfa66619bce0e584 https://github.com/galaxyproject/galaxy/commit/6ca6f9019ee034550d8da1eedfa6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/util/postfork.py Log Message: ----------- Merge pull request #5 from dannon/uwsgi-fork Add a warning when it is detected that a process is uwsgi based but u… Commit: d87fbdd5b80b110d3f0a0f8805b63eb2246a28cb https://github.com/galaxyproject/galaxy/commit/d87fbdd5b80b110d3f0a0f8805b6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/queues.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/watcher.py A lib/galaxy/util/postfork.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/tool_shed/galaxy_install/update_repository_manager.py Log Message: ----------- Merge pull request #2774 from natefoo/uwsgi-fork [16.07] Create a uWSGI postfork function registry and start the tool conf watcher thread post-fork Compare: https://github.com/galaxyproject/galaxy/compare/0719d83837aa...d87fbdd5b80b

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[galaxyproject/galaxy] 78c58f: Add column names to BED datatype so that column na...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 78c58f00f7eb69229e4f3a03130fa07434e4c154 https://github.com/galaxyproject/galaxy/commit/78c58f00f7eb69229e4f3a03130f… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Add column names to BED datatype so that column names are displayed in dataset viewer. Commit: d20828b685e5d70fcf2c15b4fc7555be60d446e9 https://github.com/galaxyproject/galaxy/commit/d20828b685e5d70fcf2c15b4fc75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #2784 from jgoecks/bed_col_names Add column names to BED datatype so that column names are displayed i… Compare: https://github.com/galaxyproject/galaxy/compare/6fb006c460da...d20828b685e5

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[galaxyproject/galaxy] 87038d: Ensure proper filtering of dataset when injecting ...
by GitHub 15 Aug '16

15 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87038d275acf46d84c1c8c110742a44002b6bdf3 https://github.com/galaxyproject/galaxy/commit/87038d275acf46d84c1c8c110742… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Ensure proper filtering of dataset when injecting input data on workflow initialization Commit: e614a6e6e4300d361d8b861a733e312f82e59b5a https://github.com/galaxyproject/galaxy/commit/e614a6e6e4300d361d8b861a733e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Improve initial value injection, adjust former run form Commit: 6fb006c460daca657a429ae78e63add6c48ef151 https://github.com/galaxyproject/galaxy/commit/6fb006c460daca657a429ae78e63… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-15 (Mon, 15 Aug 2016) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2777 from guerler/fix_filter_set Ensure proper filtering of dataset when injecting input data on workflow initialization Compare: https://github.com/galaxyproject/galaxy/compare/3b848891e5cf...6fb006c460da

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