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

[galaxyproject/galaxy] 974a9a: Add sample supervisor config
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 974a9adc1b16f54be1013cdd874dcfba5a352991 https://github.com/galaxyproject/galaxy/commit/974a9adc1b16f54be1013cdd874d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: A contrib/galaxy_supervisor.conf Log Message: ----------- Add sample supervisor config for galaxy served by uwsgi, with seperate handlers. Commit: 0de883271567f2acf59f77fe0bc69baa1adcf3ce https://github.com/galaxyproject/galaxy/commit/0de883271567f2acf59f77fe0bc6… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M contrib/galaxy_supervisor.conf Log Message: ----------- Change program name to galaxy_web Commit: 5523d8060fdfd5ef9792dadc41fa9af6118574d8 https://github.com/galaxyproject/galaxy/commit/5523d8060fdfd5ef9792dadc41fa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: A contrib/galaxy_supervisor.conf Log Message: ----------- Merge pull request #2096 from mvdbeek/supervisor_uwsgi_contrib Add sample supervisor config Compare: https://github.com/galaxyproject/galaxy/compare/753b302df0fe...5523d8060fdf

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[galaxyproject/galaxy] 7cf0a8: Run external local set_metadata jobs in the job's ...
by GitHub 06 Apr '16

06 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7cf0a80d192ad876c46154d3996672a676c43fff https://github.com/galaxyproject/galaxy/commit/7cf0a80d192ad876c46154d39966… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Run external local set_metadata jobs in the job's working directory, because metadata temp files will be created in the cwd. Previously this would most likely be the Galaxy root directory, Which Was Bad. Commit: 753b302df0fef8eb6752968ef4371bc7c14e9ebc https://github.com/galaxyproject/galaxy/commit/753b302df0fef8eb6752968ef437… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Merge pull request #2094 from natefoo/local-set-meta Run external local set_metadata jobs in the job's working directory Compare: https://github.com/galaxyproject/galaxy/compare/4138860bfdaf...753b302df0fe

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[galaxyproject/infrastructure-playbook] da4c89: Buncha updates for Jetstream
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: da4c89f371b4c036cb2a26555fff60d711b95946 https://github.com/galaxyproject/infrastructure-playbook/commit/da4c89f371b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M ansible.cfg A galaxyenv/group_vars/cvmfsstratum1servers.yml M galaxyenv/inventory A jetstreamiuenv/files/slurm/launch A jetstreamiuenv/files/slurm/slurm.conf.elastic A jetstreamiuenv/files/slurm/terminate A jetstreamiuenv/group_vars/all.yml A jetstreamiuenv/group_vars/cvmfsclients.yml A jetstreamiuenv/group_vars/galaxynodes.yml A jetstreamiuenv/group_vars/slurmclients.yml A jetstreamiuenv/group_vars/slurmservers.yml A jetstreamiuenv/instance_inventory A jetstreamiuenv/inventory A jetstreamiuenv/launch.yml A jetstreamiuenv/playbook.yml A jetstreamiuenv/secret_group_vars/slurmclients.yml A jetstreamiuenv/templates/slurm/slurm.conf.j2 A jetstreamiuenv/terminate.yml M roles/cvmfs/handlers/main.yml M roles/cvmfs/tasks/client.yml M roles/cvmfs/tasks/localproxy.yml M roles/cvmfs/tasks/main.yml R roles/cvmfs/tasks/server.yml A roles/cvmfs/tasks/stratum1.yml R roles/cvmfs/templates/squid.conf.j2 A roles/cvmfs/templates/stratum1_squid.conf.j2 M roles/cvmfs/vars/main.yml A roles/jetstream_nfs/handlers/main.yml A roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/tasks/server.yml A roles/jetstream_nfs/vars/main.yml A roles/slurm/handlers/main.yml A roles/slurm/tasks/elastic.yml A roles/slurm/tasks/main.yml A roles/slurm/templates/slurmdbd.conf.j2 A roles/slurm/vars/debian.yml A roles/slurm/vars/redhat.yml A taccenv/group_vars/galaxynodes.yml M taccenv/playbook.yml Log Message: ----------- Buncha updates for Jetstream

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[galaxyproject/galaxy] 3b31f2: Fix deps.command.download_command on Mac OS X.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3b31f23eb6a69ea4e4a35e02745444910635da75 https://github.com/galaxyproject/galaxy/commit/3b31f23eb6a69ea4e4a35e027454… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Fix deps.command.download_command on Mac OS X. Previously -O- and --recursive would be used together - this doesn't seem to be possible on Mac OS X. See issue https://github.com/galaxyproject/planemo/issues/431. Commit: 4138860bfdaff9cf0fb4cdb0a7ea5068ddf1c5d7 https://github.com/galaxyproject/galaxy/commit/4138860bfdaff9cf0fb4cdb0a7ea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_util.py M test/unit/tools/test_conda_resolution.py Log Message: ----------- Merge pull request #2075 from jmchilton/conda_download_fixes Fix deps.command.download_command on Mac OS X. Compare: https://github.com/galaxyproject/galaxy/compare/d6d216c92efb...4138860bfdaf

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[galaxyproject/galaxy] 53f178: Allow setting job_conf path for functional tests.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 53f1782964d0fe447582d6f04a87ef0d6d8c5455 https://github.com/galaxyproject/galaxy/commit/53f1782964d0fe447582d6f04a87… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M run_tests.sh M test/base/driver_util.py Log Message: ----------- Allow setting job_conf path for functional tests. Commit: 7aa2d6840a8d0094c89a53cef06423701b677211 https://github.com/galaxyproject/galaxy/commit/7aa2d6840a8d0094c89a53cef064… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py A test/base/integration_util.py A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py Log Message: ----------- Implement IntegrationTestCase and EmbeddedPulsarTestCase. IntegrationTestCases differ from functional tests in that they start up a Galaxy instance configured on a per test class basis - so this new class of "integration tests" can test configuration modalities of Galaxy that cannot be tested with traditional Galaxy functional tests. Commit: 40e123b84b6825882f9172c212258e809bd73961 https://github.com/galaxyproject/galaxy/commit/40e123b84b6825882f9172c21225… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fixup embedded Pulsar job runner based on @mvdbeek's comments. Commit: bdb41005c82678933656d651484cd1b9efeb55d1 https://github.com/galaxyproject/galaxy/commit/bdb41005c82678933656d651484c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Fix pulsar_conf/pulsar_config problem. One was being validated and the other was being read and documented. Commit: 2bd4de2025e55a9fc02ed3f74fbf297279e9d04f https://github.com/galaxyproject/galaxy/commit/2bd4de2025e55a9fc02ed3f74fbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M test/integration/__init__.py M test/integration/embedded_pulsar_job_conf.xml Log Message: ----------- Fix things found by @mvdbeek Commit: d6d216c92efb973c9f03772fdab7ac51a3688692 https://github.com/galaxyproject/galaxy/commit/d6d216c92efb973c9f03772fdab7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M run_tests.sh M scripts/functional_tests.py M test/base/driver_util.py A test/base/integration_util.py A test/integration/__init__.py A test/integration/embedded_pulsar_job_conf.xml A test/integration/test_pulsar_embedded.py Log Message: ----------- Merge pull request #2078 from jmchilton/embed_dev Enhancements for Pulsar Embedded Runner Compare: https://github.com/galaxyproject/galaxy/compare/8d703e30a029...d6d216c92efb

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[galaxyproject/galaxy] a93532: Patch in visual separation of section parameters
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a935322d4db92a7a516276c77726ba482fbdc1a7 https://github.com/galaxyproject/galaxy/commit/a935322d4db92a7a516276c77726… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 8d703e30a029c7531b8ff67ce8bf54eb1422b761 https://github.com/galaxyproject/galaxy/commit/8d703e30a029c7531b8ff67ce8bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2091 from erasche/fix_sections_001 Patch in visual separation of section parameters Compare: https://github.com/galaxyproject/galaxy/compare/118e2230276e...8d703e30a029

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[galaxyproject/galaxy] 2346b3: Fix job_wrapper.cleanup_job.
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2346b323315cc106745cc52b79f0a4fd2462e401 https://github.com/galaxyproject/galaxy/commit/2346b323315cc106745cc52b79f0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Fix job_wrapper.cleanup_job. Broken in 16.04 with 81b5ca564ac7cdd855cb74dad8e98abc83a8efdc in PR #1688. Minor. Commit: 118e2230276ea582b136a84235813b8b582faf44 https://github.com/galaxyproject/galaxy/commit/118e2230276ea582b136a8423581… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #2089 from jmchilton/cleanup_job Fix job_wrapper.cleanup_job. Compare: https://github.com/galaxyproject/galaxy/compare/13af4a11a13c...118e2230276e

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[galaxyproject/galaxy] 2a53be: Show sections in workflow run
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109 https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2092 from erasche/workflow-section-backport [16.01] Workflow section fix backport Compare: https://github.com/galaxyproject/galaxy/compare/65a7ebee2336...040410b1d3f0

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[galaxyproject/galaxy] 1114f4: Show sections in workflow run
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1114f476b65330388ab6f133756c2473c6835716 https://github.com/galaxyproject/galaxy/commit/1114f476b65330388ab6f133756c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 13af4a11a13c3d8a12a49b29734d5df7bea5932a https://github.com/galaxyproject/galaxy/commit/13af4a11a13c3d8a12a49b29734d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2087 from guerler/fix_sections_000 Show sections in workflow run Compare: https://github.com/galaxyproject/galaxy/compare/e37761346625...13af4a11a13c

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[galaxyproject/galaxy] 3c8278: Implement new GIE proxy
by GitHub 05 Apr '16

05 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3c8278c1bae103d5aaa3d264748c5f9049474dba https://github.com/galaxyproject/galaxy/commit/3c8278c1bae103d5aaa3d264748c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Implement new GIE proxy This provides an alternative proxy to the original NodeJS proxy. The implementation is done in golang, which has the nice property of compiling to a single binary. While it's a negative in terms of number of devteam who write that language, I'd argue it's not that much worse than nodejs in terms of accessibility. Features include: - Simple rest-ish API instead of file-based IPC - Automatic culling of containers, no more monitor_traffic.sh hacks - Admin configurable, cross GIE timeout setting Commit: 7830ee8724f488e1ea3efe49a8557aed74114811 https://github.com/galaxyproject/galaxy/commit/7830ee8724f488e1ea3efe49a855… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py Log Message: ----------- Address @mvdbeek's issues Commit: 5bfb87204841ddf566d078555e9f0458dd407de5 https://github.com/galaxyproject/galaxy/commit/5bfb87204841ddf566d078555e9f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Remove logging Commit: d7ed11477bbe50e4f058f389ebb753b412ac7000 https://github.com/galaxyproject/galaxy/commit/d7ed11477bbe50e4f058f389ebb7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Whitespace changes for travis Commit: 4c6cf5d4f9e2ecec8eb379ef8075ef20fb1da8fc https://github.com/galaxyproject/galaxy/commit/4c6cf5d4f9e2ecec8eb379ef8075… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Typo in config causes first run to fail Commit: e37761346625aed03af3bdee337686b0e697fd7a https://github.com/galaxyproject/galaxy/commit/e37761346625aed03af3bdee3376… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #1807 from erasche/gie-go-proxy-2 Implement new GIE proxy Compare: https://github.com/galaxyproject/galaxy/compare/1543f0d92507...e37761346625

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