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

[galaxyproject/infrastructure-playbook] 10bb73: Set $GALAXY_VIRTUAL_ENV for Jetstream Pulsar.
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/blog Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 10bb73a321a4b60dfe7bfd94cf14c3e89fe4bf54 https://github.com/galaxyproject/infrastructure-playbook/commit/10bb73a321a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M jetstream_common/templates/supervisor/pulsar.j2 Log Message: ----------- Set $GALAXY_VIRTUAL_ENV for Jetstream Pulsar. Commit: dcf13819c8719182d4dd9af163e2b2d3c8539909 https://github.com/galaxyproject/infrastructure-playbook/commit/dcf13819c87… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M jetstream_common/templates/supervisor/pulsar.j2 Log Message: ----------- Merge branch 'master' into blog Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/cdcb6dd6f8…

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[galaxyproject/infrastructure-playbook] cdcb6d: Restored and modified "this file is maintained by ...
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/blog Home: https://github.com/galaxyproject/infrastructure-playbook Commit: cdcb6dd6f8b0045311dbbf4b6d4bfaaf3415c1cd https://github.com/galaxyproject/infrastructure-playbook/commit/cdcb6dd6f8b… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M galaxyenv/templates/nginx/wiki_hub_rewrites.conf.j2 Log Message: ----------- Restored and modified "this file is maintained by Ansible" comment.

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[galaxyproject/galaxy] f709dd: Add requirejs config to cachebust IE require'd fil...
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f709ddcfe6b6bad0ca03ff208195f68d4e65fdc4 https://github.com/galaxyproject/galaxy/commit/f709ddcfe6b6bad0ca03ff208195… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Add requirejs config to cachebust IE require'd files. Commit: 03394d44c92d2bec790c37b59e50872c072f99e6 https://github.com/galaxyproject/galaxy/commit/03394d44c92d2bec790c37b59e50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map 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/scripts/mvc/workflow/workflow.js Log Message: ----------- Support workflow list messaging Commit: fa4c1b5da7aa2c035bb5685d150b3cb8f952dd6a https://github.com/galaxyproject/galaxy/commit/fa4c1b5da7aa2c035bb5685d150b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- More fixes for the workflow list page, and some general cleanup. Commit: 63022e6718f2e9206e7a94b63949a8e97d08d352 https://github.com/galaxyproject/galaxy/commit/63022e6718f2e9206e7a94b63949… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Drop stray debugging statement. Commit: 8820e3bc583ea140f1c154bd35c2ccc905ab4fb8 https://github.com/galaxyproject/galaxy/commit/8820e3bc583ea140f1c154bd35c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Rebuild client. Commit: 266361d1517b60177889e7a34a2f32cc0a6a938f https://github.com/galaxyproject/galaxy/commit/266361d1517b60177889e7a34a2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js.map Log Message: ----------- Minor formatting. Commit: 958d917cb51c2ade15d69279d893489d37c8d976 https://github.com/galaxyproject/galaxy/commit/958d917cb51c2ade15d69279d893… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Display error message when workflow loading fails Commit: 407da92f88ac859d3f9b259be83640516159fe15 https://github.com/galaxyproject/galaxy/commit/407da92f88ac859d3f9b259be836… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map 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/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #4716 from dannon/workflow_list_messaging [17.09] Add message (error and info) display to workflows display list. Commit: 7167c0434b713562293267f7c8adebff3920d6cc https://github.com/galaxyproject/galaxy/commit/7167c0434b713562293267f7c8ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #4714 from dannon/cachebust_ies [17.09] Cachebust IE require'd files (jupyter.js, etc). Commit: f4941e54224d67880e3d4a9fee03d75a049a65f1 https://github.com/galaxyproject/galaxy/commit/f4941e54224d67880e3d4a9fee03… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M config/plugins/interactive_environments/common/templates/ie.mako M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map 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/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge branch 'release_17.09' into dev Conflicts: static/scripts/bundled/admin.bundled.js static/scripts/bundled/admin.bundled.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/1f0086de6788...f4941e54224d

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[galaxyproject/usegalaxy-playbook] c36464: Convert NVC dynamic rule dos to unix line endings
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3646487129e06ae5f4488a85c50c34874ff105a https://github.com/galaxyproject/usegalaxy-playbook/commit/c3646487129e06ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/nvc_dynamic_memory.py Log Message: ----------- Convert NVC dynamic rule dos to unix line endings Commit: 4cd46aea3fbf397f864641aa05b873624090fc95 https://github.com/galaxyproject/usegalaxy-playbook/commit/4cd46aea3fbf397f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/nvc_dynamic_memory.py Log Message: ----------- Fix nvc dynamic rule name after recent job_conf.xml macroization. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b51faf9bdb13...…

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[galaxyproject/galaxy] c421f2: Log more information on command execution
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c421f29d851c8ebdbd29d87fe378ef06a78aaecf https://github.com/galaxyproject/galaxy/commit/c421f29d851c8ebdbd29d87fe378… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Log more information on command execution So we can tell *why* it failed on not just that it failed. Commit: 955206b05208f920f0db60473c90a0e20ca6e181 https://github.com/galaxyproject/galaxy/commit/955206b05208f920f0db60473c90… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Another debugging statement Commit: 85533747050494cd5c2ddb749506b75e40e6bff0 https://github.com/galaxyproject/galaxy/commit/85533747050494cd5c2ddb749506… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Unicodify anything logged due to the french Commit: 7e7369c168991302f4a3b434cc25d8da934f5506 https://github.com/galaxyproject/galaxy/commit/7e7369c168991302f4a3b434cc25… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- collapse logging + : Commit: 08b90d699d72358c89104643f1859869c5d4dffc https://github.com/galaxyproject/galaxy/commit/08b90d699d72358c89104643f185… Author: E Rasche <hxr(a)hx42.org> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Move sleep Commit: 1f0086de6788c904d94debb3da23644543d9a503 https://github.com/galaxyproject/galaxy/commit/1f0086de6788c904d94debb3da23… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Merge pull request #4720 from erasche/integrity-exceptions Add logging during for script integrity exceptions Compare: https://github.com/galaxyproject/galaxy/compare/9a0511e8839c...1f0086de6788

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[galaxyproject/galaxy] f709dd: Add requirejs config to cachebust IE require'd fil...
by GitHub 28 Sep '17

28 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: f709ddcfe6b6bad0ca03ff208195f68d4e65fdc4 https://github.com/galaxyproject/galaxy/commit/f709ddcfe6b6bad0ca03ff208195… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Add requirejs config to cachebust IE require'd files. Commit: 7167c0434b713562293267f7c8adebff3920d6cc https://github.com/galaxyproject/galaxy/commit/7167c0434b713562293267f7c8ad… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #4714 from dannon/cachebust_ies [17.09] Cachebust IE require'd files (jupyter.js, etc). Compare: https://github.com/galaxyproject/galaxy/compare/407da92f88ac...7167c0434b71

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[galaxyproject/galaxy] 03394d: Support workflow list messaging
by GitHub 27 Sep '17

27 Sep '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 03394d44c92d2bec790c37b59e50872c072f99e6 https://github.com/galaxyproject/galaxy/commit/03394d44c92d2bec790c37b59e50… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map 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/scripts/mvc/workflow/workflow.js Log Message: ----------- Support workflow list messaging Commit: fa4c1b5da7aa2c035bb5685d150b3cb8f952dd6a https://github.com/galaxyproject/galaxy/commit/fa4c1b5da7aa2c035bb5685d150b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- More fixes for the workflow list page, and some general cleanup. Commit: 63022e6718f2e9206e7a94b63949a8e97d08d352 https://github.com/galaxyproject/galaxy/commit/63022e6718f2e9206e7a94b63949… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Drop stray debugging statement. Commit: 8820e3bc583ea140f1c154bd35c2ccc905ab4fb8 https://github.com/galaxyproject/galaxy/commit/8820e3bc583ea140f1c154bd35c2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Rebuild client. Commit: 266361d1517b60177889e7a34a2f32cc0a6a938f https://github.com/galaxyproject/galaxy/commit/266361d1517b60177889e7a34a2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js.map Log Message: ----------- Minor formatting. Commit: 958d917cb51c2ade15d69279d893489d37c8d976 https://github.com/galaxyproject/galaxy/commit/958d917cb51c2ade15d69279d893… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Display error message when workflow loading fails Commit: 407da92f88ac859d3f9b259be83640516159fe15 https://github.com/galaxyproject/galaxy/commit/407da92f88ac859d3f9b259be836… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map 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/scripts/mvc/workflow/workflow.js Log Message: ----------- Merge pull request #4716 from dannon/workflow_list_messaging [17.09] Add message (error and info) display to workflows display list. Compare: https://github.com/galaxyproject/galaxy/compare/d41f4ce0ec89...407da92f88ac

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[galaxyproject/usegalaxy-playbook] b51faf: Fix Stampede-only jobs
by GitHub 27 Sep '17

27 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b51faf9bdb1333357ab654e47a995e2155f34acf https://github.com/galaxyproject/usegalaxy-playbook/commit/b51faf9bdb133335… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Fix Stampede-only jobs

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[galaxyproject/usegalaxy-playbook] fdcf1f: Pulsar updates and fixes
by GitHub 27 Sep '17

27 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fdcf1fc04614df25bca3709a8ed51717b0b2f5f0 https://github.com/galaxyproject/usegalaxy-playbook/commit/fdcf1fc04614df25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: A env/common/files/pulsar/config/stampede_dependency_resolvers_conf.xml M env/main/host_vars/br005.bridges.psc.edu.yml M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Pulsar updates and fixes Commit: 34c076d9fc0d31d0f2f271c33d48efe6e6a083e1 https://github.com/galaxyproject/usegalaxy-playbook/commit/34c076d9fc0d31d0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Updated Main again Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d0edc3f5ca28...…

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[galaxyproject/infrastructure-playbook] 10bb73: Set $GALAXY_VIRTUAL_ENV for Jetstream Pulsar.
by GitHub 27 Sep '17

27 Sep '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 10bb73a321a4b60dfe7bfd94cf14c3e89fe4bf54 https://github.com/galaxyproject/infrastructure-playbook/commit/10bb73a321a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-09-27 (Wed, 27 Sep 2017) Changed paths: M jetstream_common/templates/supervisor/pulsar.j2 Log Message: ----------- Set $GALAXY_VIRTUAL_ENV for Jetstream Pulsar.

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