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

[galaxyproject/infrastructure-playbook] b787af: Use autofs for mounting Jetstream scratch on nodes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b787af633f4b3431e536b34e2080917cc4b96b95 https://github.com/galaxyproject/infrastructure-playbook/commit/b787af633f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/slurmclients.yml A roles/jetstream_nfs/tasks/client.yml M roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/templates/auto.jetstream.j2 Log Message: ----------- Use autofs for mounting Jetstream scratch on nodes

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[galaxyproject/infrastructure-playbook] 938fd7: Use autofs for mounting Jetstream scratch on nodes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 938fd7d2c7c645277c46e63a618d597010040f36 https://github.com/galaxyproject/infrastructure-playbook/commit/938fd7d2c7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamiuenv/group_vars/galaxynodes.yml M jetstreamtaccenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/galaxynodes.yml A roles/jetstream_nfs/tasks/client.yml M roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/templates/auto.jetstream.j2 Log Message: ----------- Use autofs for mounting Jetstream scratch on nodes

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[galaxyproject/infrastructure-playbook] df05c3: Use autofs for mounting Jetstream scratch on nodes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: df05c32750ea5a0da4b8160fa34bea293922e636 https://github.com/galaxyproject/infrastructure-playbook/commit/df05c32750e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M jetstreamtaccenv/group_vars/galaxynodes.yml A roles/jetstream_nfs/tasks/client.yml M roles/jetstream_nfs/tasks/main.yml A roles/jetstream_nfs/templates/auto.jetstream.j2 Log Message: ----------- Use autofs for mounting Jetstream scratch on nodes

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[galaxyproject/galaxy] 10ef0a: HTCondor and Docker documentation
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10ef0a3b00681dbab09119cc057a3ebe47e3d4f9 https://github.com/galaxyproject/galaxy/commit/10ef0a3b00681dbab09119cc057a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- HTCondor and Docker documentation Commit: ba409e75181224c80f0acf02530cac31fe28461c https://github.com/galaxyproject/galaxy/commit/ba409e75181224c80f0acf02530c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- enable HTCondor Docker integration Commit: 3ab43e38f5b2d63c300e99635234051956905f94 https://github.com/galaxyproject/galaxy/commit/3ab43e38f5b2d63c300e99635234… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-04-30 (Sat, 30 Apr 2016) Changed paths: M test/functional/tools/catDocker.xml Log Message: ----------- add new Docker Image. We need to have bash inside of Docker. Commit: ead96a55a9d05602a7b241d2d8b8acf557ce9425 https://github.com/galaxyproject/galaxy/commit/ead96a55a9d05602a7b241d2d8b8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-01 (Sun, 01 May 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add the ability to set the default handler and destination via environment variables. Commit: 7bd595b8f1caf4ea5085a41ba8129653d48f83a7 https://github.com/galaxyproject/galaxy/commit/7bd595b8f1caf4ea5085a41ba812… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M test/functional/tools/catDocker.xml Log Message: ----------- Revert "add new Docker Image. We need to have bash inside of Docker." This reverts commit 3ab43e38f5b2d63c300e99635234051956905f94. Commit: 917c882255ff1261bb99bb4bfc8bd1e165e26b96 https://github.com/galaxyproject/galaxy/commit/917c882255ff1261bb99bb4bfc8b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Revise HTCondor Docker image resolution. Bring inline with the rest of the job runner's Docker image resolution stuff. Order of reosolution is: - Use destination specified override if found: docker_container_id_override - Use the tool specified container if not found and no override: see tool - Else - use docker_default_container_id. This adjusts the documentation to reflect this and make the the parameters more consistent throughout. I've modified this so docker_image (the old name introduced by the Docker Condor PR) still works - but I have left it undocumented intentionally for consistency. Commit: 8e6211aeb1bc3ffa696d61be89954d6e68215be4 https://github.com/galaxyproject/galaxy/commit/8e6211aeb1bc3ffa696d61be8995… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #10 from jmchilton/htcondor_docker Revise HTCondor Docker image resolution. Commit: c2ea4ee5266370ef1378df922af5a0c96d0f835c https://github.com/galaxyproject/galaxy/commit/c2ea4ee5266370ef1378df922af5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #2278 from bgruening/htcondor_docker HTCondor Docker Integration Compare: https://github.com/galaxyproject/galaxy/compare/6fc2ae42cd4f...c2ea4ee52663

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[galaxyproject/usegalaxy-playbook] 2f7c3b: Main mutable config changes
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2f7c3b4a674701fc1a1bc7577351f210d3986c9c https://github.com/galaxyproject/usegalaxy-playbook/commit/2f7c3b4a674701fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable config changes

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[galaxyproject/usegalaxy-playbook] ca7935: Store Main mutable configs in NFS so they don't ha...
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ca793528240877fe9d2b09099adce6722be9c43f https://github.com/galaxyproject/usegalaxy-playbook/commit/ca793528240877fe… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M production/group_vars/galaxyservers.yml M roles/usegalaxy/tasks/main.yml M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Store Main mutable configs in NFS so they don't have to be distributed.

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[galaxyproject/usegalaxy-playbook] 4bd600: Add extra headers for web-02->web-01 proxy for lau...
by GitHub 17 May '16

17 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4bd6000817455d34514161e718e06481a77e9ef0 https://github.com/galaxyproject/usegalaxy-playbook/commit/4bd6000817455d34… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M templates/nginx/usegalaxy.j2 Log Message: ----------- Add extra headers for web-02->web-01 proxy for launching Jupyter (this is necessary for the returned page to have the correct host in the IE links).

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[galaxyproject/galaxy] 90c48f: update check for Conda env.
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90c48ff6e314c77da75deab8ca716bf14065d089 https://github.com/galaxyproject/galaxy/commit/90c48ff6e314c77da75deab8ca71… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- update check for Conda env. Commit: ea2e9163d6827de2e1eb4208db205017c0d94dc4 https://github.com/galaxyproject/galaxy/commit/ea2e9163d6827de2e1eb4208db20… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- changed grep statement to match 2 patterns Now matches both "anaconda" and "continuum analytics" Commit: 6fc2ae42cd4fb20daa7c3927fb52834ca5771580 https://github.com/galaxyproject/galaxy/commit/6fc2ae42cd4fb20daa7c3927fb52… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #2295 from matthdsm/patch-4 update check for Conda env. Compare: https://github.com/galaxyproject/galaxy/compare/df2a068a3bc0...6fc2ae42cd4f

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[galaxyproject/galaxy] 1a6f1a: Update README to remove 2.6
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a6f1a36f4a157d0e5109189f982df1a5083dbbb https://github.com/galaxyproject/galaxy/commit/1a6f1a36f4a157d0e5109189f982… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M README.rst Log Message: ----------- Update README to remove 2.6 Hi :), Galaxy is not compatible with Python 2.6 since 16.01, right? What do we think about removing it from this README? We could also say 2.6 for Galaxy version under 16.01, and 2.7 for upper. Commit: df2a068a3bc0e86a0895e85b9ee5a5700eb8e22e https://github.com/galaxyproject/galaxy/commit/df2a068a3bc0e86a0895e85b9ee5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M README.rst Log Message: ----------- Merge pull request #2367 from remimarenco/patch-6 Update README to remove 2.6 Compare: https://github.com/galaxyproject/galaxy/compare/180eeeafe338...df2a068a3bc0

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[galaxyproject/galaxy] c749e1: Revise portlet view
by GitHub 17 May '16

17 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c749e13973ee8a5f46a486411fbfd14fdda578bd https://github.com/galaxyproject/galaxy/commit/c749e13973ee8a5f46a486411fbf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-05-16 (Mon, 16 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Revise portlet view Commit: 180eeeafe3385777861d06241c97633145fd4f82 https://github.com/galaxyproject/galaxy/commit/180eeeafe3385777861d06241c97… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-17 (Tue, 17 May 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/style/less/ui.less M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/ui/ui-portlet.js M static/style/blue/base.css Log Message: ----------- Merge branch 'revise_portlet_000' into dev Compare: https://github.com/galaxyproject/galaxy/compare/665809f25cb0...180eeeafe338

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