galaxy-commits October 2015

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] e3364d: Update comment in sample.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e3364d6db428d0695ce978dfa0604e775da11f67 https://github.com/galaxyproject/galaxy/commit/e3364d6db428d0695ce978dfa060… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Update comment in sample. Commit: 51a3f5414064d0b927023cb9e0096995e0470b8d https://github.com/galaxyproject/galaxy/commit/51a3f5414064d0b927023cb9e009… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #841 from dannon/default_debug_off Update comment in sample. Compare: https://github.com/galaxyproject/galaxy/compare/a92ed830ee66...51a3f5414064

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[galaxyproject/galaxy] 1564dc: Swap debug mode to be off by default in galaxy.ini...
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1564dc665be8e2a44cb3298f22e0d70811205c15 https://github.com/galaxyproject/galaxy/commit/1564dc665be8e2a44cb3298f22e0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Swap debug mode to be off by default in galaxy.ini.sample. Commit: a92ed830ee66719708b062b39f64092741a83975 https://github.com/galaxyproject/galaxy/commit/a92ed830ee66719708b062b39f64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #840 from dannon/default_debug_off Swap debug mode to be off by default in galaxy.ini.sample. Compare: https://github.com/galaxyproject/galaxy/compare/a47f9defe322...a92ed830ee66

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[galaxyproject/galaxy] 4e3fe5: Fix to a5e97e6: correctly pass in dom fragment to ...
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e3fe5012f295e9f64c81b914332068a8a04d8fb https://github.com/galaxyproject/galaxy/commit/4e3fe5012f295e9f64c81b914332… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Fix to a5e97e6: correctly pass in dom fragment to setUpBehaviors (fixes multiselect btn and name editing Commit: a47f9defe32211b8b589794a7a761889b053326c https://github.com/galaxyproject/galaxy/commit/a47f9defe32211b8b589794a7a76… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel-edit-current.js M static/maps/mvc/history/history-panel-edit-current.js.map M static/scripts/mvc/history/history-panel-edit-current.js Log Message: ----------- Merge pull request #834 from carlfeberhard/fix.multiselect Fix to a5e97e6: correctly pass in dom fragment to setUpBehaviors (fix… Compare: https://github.com/galaxyproject/galaxy/compare/02962ae64680...a47f9defe322

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[galaxyproject/usegalaxy-playbook] 3b6a3b: update Test mutable confs
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3b6a3b14c56fe59d3f6c9bd9b8cc7ae1ee10e381 https://github.com/galaxyproject/usegalaxy-playbook/commit/3b6a3b14c56fe59d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- update Test mutable confs

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[galaxyproject/galaxy]
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/pr/475 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 8af833: Fix a potentially problematic file operation.
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8af833cb347a02212403e058cd7f8cc9d263499d https://github.com/galaxyproject/galaxy/commit/8af833cb347a02212403e058cd7f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Fix a potentially problematic file operation. It might be causing intermittent test failures when running this code in Docker containers, we are unsure. Commit: 02962ae646805816f83a649c39d4c9336baf7056 https://github.com/galaxyproject/galaxy/commit/02962ae646805816f83a649c39d4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/local.py Log Message: ----------- Merge pull request #830 from jmchilton/local_close Improved file handling in local runner. Compare: https://github.com/galaxyproject/galaxy/compare/b3a375642476...02962ae64680

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[galaxyproject/galaxy] 567348: Statsd middleware for request timing.
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 56734878e7bce2954933b23d4c3c4bc8fd640a5b https://github.com/galaxyproject/galaxy/commit/56734878e7bce2954933b23d4c3c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py A lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Statsd middleware for request timing. Commit: e710c46f2461eee2303f219b3e2c6081f932d7a4 https://github.com/galaxyproject/galaxy/commit/e710c46f2461eee2303f219b3e2c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Fix namespacing of events Commit: 1b841a9aa408fbd6e555cbbd8b298cdbd07e4590 https://github.com/galaxyproject/galaxy/commit/1b841a9aa408fbd6e555cbbd8b29… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- Tweak docstring Commit: 52a51af4edb7b6488f1823be5e2702438216d96b https://github.com/galaxyproject/galaxy/commit/52a51af4edb7b6488f1823be5e27… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix middleware application message. Commit: fc69247d500bda21c6e766b54495179208039e10 https://github.com/galaxyproject/galaxy/commit/fc69247d500bda21c6e766b54495… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix default statsd port. Commit: c6794e62c594cf7090323cdc154e1587f2491e85 https://github.com/galaxyproject/galaxy/commit/c6794e62c594cf7090323cdc154e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- In lieu of rolling an egg, just test for statsd when middleware is wrapped. Commit: 72330cc316ede4ef083c2c92b5162e03994df37b https://github.com/galaxyproject/galaxy/commit/72330cc316ede4ef083c2c92b516… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py Log Message: ----------- 'Fix' for unit tests. Commit: 3fa78449563f1e6c050172268371ceca0f03d95f https://github.com/galaxyproject/galaxy/commit/3fa78449563f1e6c050172268371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Opt for failing instead of continuing to run Galaxy if statsd middleware is configured but module is not available. Commit: b3a37564247623181422e68766e7ccd878b01be0 https://github.com/galaxyproject/galaxy/commit/b3a37564247623181422e68766e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py A lib/galaxy/web/framework/middleware/statsd.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #821 from dannon/statsd Request timing middleware via statsd Compare: https://github.com/galaxyproject/galaxy/compare/e9961d3dfec0...b3a375642476

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[galaxyproject/galaxy] a8bc87: Remove test broken after #786.
by GitHub 02 Oct '15

02 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8bc87473672bf3def3dc101bd515cc608664a72 https://github.com/galaxyproject/galaxy/commit/a8bc87473672bf3def3dc101bd51… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Remove test broken after #786. Commit: e9961d3dfec0b349aba7b8fad899cc923cd3fde2 https://github.com/galaxyproject/galaxy/commit/e9961d3dfec0b349aba7b8fad899… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Merge pull request #828 from nsoranzo/dev Remove test broken after #786. Compare: https://github.com/galaxyproject/galaxy/compare/5592422d01ea...e9961d3dfec0

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[galaxyproject/usegalaxy-playbook] 39ade7: Update Main datatypes_conf.xml, add hg38 to ucsc_b...
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 39ade7036f13ce4ae7796f44b66395be5a148887 https://github.com/galaxyproject/usegalaxy-playbook/commit/39ade7036f13ce4a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M files/galaxy/usegalaxy.org/config/ucsc_build_sites.txt M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update Main datatypes_conf.xml, add hg38 to ucsc_builds_sites.

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[galaxyproject/usegalaxy-playbook] 659105: Mutable configs on Main
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 659105dad2a5d339e621f6d0cb2def74de1e54fb https://github.com/galaxyproject/usegalaxy-playbook/commit/659105dad2a5d339… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-01 (Thu, 01 Oct 2015) 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: ----------- Mutable configs on Main

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galaxy-commits October 2015