- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 2210f8: Remove run_functional_tests.sh.
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2210f83da95b702ea10f7809b29ee77d54fc1529 https://github.com/galaxyproject/galaxy/commit/2210f83da95b702ea10f7809b29e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R run_functional_tests.sh Log Message: ----------- Remove run_functional_tests.sh. It has been deprecated who a while and removed once already - hopefully now we can kill it. Commit: 596f9116f25f384899f9c7acb5517d57b88ca358 https://github.com/galaxyproject/galaxy/commit/596f9116f25f384899f9c7acb551… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Use framework test tools for --api and --casperjs tests. These tests are explicitly designed to test the framework and use a tool panel. ``sh run_tests.sh`` and ``sh run_tests.sh -id`` are meant to test Galaxy's configuration to some degree, and other tests qunit, unit, and toolshed do not depend on the toolbox. Commit: 0a83a244f170226ec02f41a9972bd9bfcb261449 https://github.com/galaxyproject/galaxy/commit/0a83a244f170226ec02f41a9972b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: R run_functional_tests.sh M run_tests.sh Log Message: ----------- Merge pull request #844 from jmchilton/run_test_adjustments More small adjustments to test script. Compare: https://github.com/galaxyproject/galaxy/compare/7dcd2636fd83...0a83a244f170

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[galaxyproject/galaxy] f64a23: initial implementation of library search
by GitHub 05 Oct '15

05 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f64a23fbe16d2af956840ffef673f6455700249f https://github.com/galaxyproject/galaxy/commit/f64a23fbe16d2af956840ffef673… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- initial implementation of library search Commit: 91ef04a25bdc5962ce650d925db5f8a94c345d06 https://github.com/galaxyproject/galaxy/commit/91ef04a25bdc5962ce650d925db5… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- docs, refac and indentation Commit: 7dcd2636fd83dc935306cbd405091c60c1d54bdf https://github.com/galaxyproject/galaxy/commit/7dcd2636fd83dc935306cbd40509… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-10-05 (Mon, 05 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js Log Message: ----------- Merge pull request #820 from martenson/lib-search Initial implementation of data library search Compare: https://github.com/galaxyproject/galaxy/compare/51a3f5414064...7dcd2636fd83

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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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[galaxyproject/galaxy] 8cc27b: Fix default value for optional select fields
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cc27b45d04da7d6298a0b63c0a9c820dc6bed03 https://github.com/galaxyproject/galaxy/commit/8cc27b45d04da7d6298a0b63c0a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix default value for optional select fields Commit: df74d2651b32f110137359d4d9b41c7c581846fd https://github.com/galaxyproject/galaxy/commit/df74d2651b32f110137359d4d9b4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Fix label text Commit: 5592422d01ea99bb0ba7c688227e38e963e96061 https://github.com/galaxyproject/galaxy/commit/5592422d01ea99bb0ba7c688227e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M lib/galaxy/tools/parameters/basic.py M static/maps/mvc/ui/ui-options.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-options.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #826 from guerler/fix_select_000 Fix default value for optional select fields Compare: https://github.com/galaxyproject/galaxy/compare/bf33c847e03e...5592422d01ea

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[galaxyproject/galaxy] b0b119: Normalize test output name.
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b0b119356b130b82c39c6c811369f002cc571614 https://github.com/galaxyproject/galaxy/commit/b0b119356b130b82c39c6c811369… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M run_tests.sh Log Message: ----------- Normalize test output name. Update toolshed, casperjs, and framework tests to produce reports with the name of run_<type>_tests.html to match functional and API tests. Commit: 49740caaa2cf00e1eeb8bfdef1939638256103a0 https://github.com/galaxyproject/galaxy/commit/49740caaa2cf00e1eeb8bfdef193… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M run_tests.sh M test/casperjs/casperjs_runner.py Log Message: ----------- Add documentation for running casperjs tests through run_tests.sh. Add option to run a specific test. Verified xunit reports work and --dockerize works for casperjs tests. Commit: bf33c847e03ed0998f493c126c011fb492b07fb0 https://github.com/galaxyproject/galaxy/commit/bf33c847e03ed0998f493c126c01… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M run_tests.sh M test/casperjs/casperjs_runner.py Log Message: ----------- Merge pull request #825 from jmchilton/db_test_fix Various small run_tests.sh fixes/enhancements. Compare: https://github.com/galaxyproject/galaxy/compare/50547177f954...bf33c847e03e

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[galaxyproject/galaxy] a5e97e: UI, histories: fix scroll position capture/restore...
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5e97e6e590c6cc387530e914af4bea8af66fe44 https://github.com/galaxyproject/galaxy/commit/a5e97e6e590c6cc387530e914af4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-01 (Thu, 01 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: ----------- UI, histories: fix scroll position capture/restore for the current history Commit: 50547177f954377d66b9193e504bdbfb01e04e7d https://github.com/galaxyproject/galaxy/commit/50547177f954377d66b9193e504b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 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 #824 from carlfeberhard/fix.history-scroll-capture UI, histories: fix scroll position capture/restore for the current hi… Compare: https://github.com/galaxyproject/galaxy/compare/de82b1236dcf...50547177f954

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[galaxyproject/galaxy] 8a30d3: Fix change_password (destination for password rese...
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a30d3add42904f1117599790d63dfa273374d51 https://github.com/galaxyproject/galaxy/commit/8a30d3add42904f1117599790d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix change_password (destination for password reset link) to work w/ require_login Commit: 76fcde3274688db10eb259cdf25dbcc0d5187262 https://github.com/galaxyproject/galaxy/commit/76fcde3274688db10eb259cdf25d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #811 from dannon/prt_fix [15.07] Fix change_password (destination for password reset link) to work w/ … Commit: 43ed7d556a4de0d8450c26848827a0dd25d5ad45 https://github.com/galaxyproject/galaxy/commit/43ed7d556a4de0d8450c26848827… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/web/framework/webapp.py M lib/pulsar/client/amqp_exchange.py M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'release_15.07' Commit: de82b1236dcf92137e9002cc9cad6e16125119fe https://github.com/galaxyproject/galaxy/commit/de82b1236dcf92137e9002cc9cad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c133078b6014...de82b1236dcf

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[galaxyproject/galaxy] e52b9a: Show tool parameter errors on initial tool form lo...
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: e52b9ac2552ea19c6e534968661382e23cc362fa https://github.com/galaxyproject/galaxy/commit/e52b9ac2552ea19c6e5349686613… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Show tool parameter errors on initial tool form load. Needed for e.g. proper rerun display behavoir. Commit: 394c3726d6ff6d515b99361465c743d7cd9651d9 https://github.com/galaxyproject/galaxy/commit/394c3726d6ff6d515b99361465c7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge pull request #802 from blankenberg/tool_error_fixes [15.07] Show tool parameter errors on initial tool form load. Commit: 6fef4465ae3f8875a1aa6153d957941dd3fd737e https://github.com/galaxyproject/galaxy/commit/6fef4465ae3f8875a1aa6153d957… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-28 (Mon, 28 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue when consuming more than one. Also, only start one acknowledgement manager thread rather than one per consumer. Commit: 8a30d3add42904f1117599790d63dfa273374d51 https://github.com/galaxyproject/galaxy/commit/8a30d3add42904f1117599790d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Fix change_password (destination for password reset link) to work w/ require_login Commit: 8c9e8686a159ec9fbee65457a8042fdcefd632f2 https://github.com/galaxyproject/galaxy/commit/8c9e8686a159ec9fbee65457a804… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #808 from natefoo/amqp_ack [15.07] [Pulsar] Resubmit AMQP acknowledgement messages to the correct queue Commit: 76fcde3274688db10eb259cdf25dbcc0d5187262 https://github.com/galaxyproject/galaxy/commit/76fcde3274688db10eb259cdf25d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M lib/galaxy/web/framework/webapp.py Log Message: ----------- Merge pull request #811 from dannon/prt_fix [15.07] Fix change_password (destination for password reset link) to work w/ … Commit: 43ed7d556a4de0d8450c26848827a0dd25d5ad45 https://github.com/galaxyproject/galaxy/commit/43ed7d556a4de0d8450c26848827… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form.js M lib/galaxy/web/framework/webapp.py M lib/pulsar/client/amqp_exchange.py M static/maps/mvc/tools/tools-form.js.map M static/scripts/mvc/tools/tools-form.js Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/759b67dfa8cc...43ed7d556a4d

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[galaxyproject/galaxy] 6592a1: Fix db initialization when galaxy.ini doesn't exis...
by GitHub 01 Oct '15

01 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6592a140899a93a54d0bff1f7944a489e746bf06 https://github.com/galaxyproject/galaxy/commit/6592a140899a93a54d0bff1f7944… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Fix db initialization when galaxy.ini doesn't exist. Commit: c133078b60146450fc9b05db8c5a4ff52af5bc95 https://github.com/galaxyproject/galaxy/commit/c133078b60146450fc9b05db8c5a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-01 (Thu, 01 Oct 2015) Changed paths: M lib/galaxy/model/orm/scripts.py Log Message: ----------- Merge pull request #822 from jmchilton/db_test_fix Fix db initialization when galaxy.ini doesn't exist. Compare: https://github.com/galaxyproject/galaxy/compare/d8ce3c25df0e...c133078b6014

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[galaxyproject/galaxy] 785f81: Add developer documentation to docs
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 785f81989627db26b3799b0e6d5123213fcec9e4 https://github.com/galaxyproject/galaxy/commit/785f81989627db26b3799b0e6d51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/dev/faq.rst A doc/source/dev/index.rst M doc/source/index.rst Log Message: ----------- Add developer documentation to docs Commit: 86c3175fcda4ff85505ecfcd78cf2b302909a7a7 https://github.com/galaxyproject/galaxy/commit/86c3175fcda4ff85505ecfcd78cf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: A doc/source/_api_quickstart.rst A doc/source/api/quickstart.rst M doc/source/api_doc.rst M doc/source/ts_api_doc.rst Log Message: ----------- Extract quickstart, reorg GX/TS Doc index Commit: 0bfa99725463f1807816e5c0bdeacf46eb186c55 https://github.com/galaxyproject/galaxy/commit/0bfa99725463f1807816e5c0bdea… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-08-26 (Wed, 26 Aug 2015) Changed paths: R doc/source/_api_quickstart.rst Log Message: ----------- Remove unused file Commit: b6105acd2b7f0957c315a63bcf083a596189383b https://github.com/galaxyproject/galaxy/commit/b6105acd2b7f0957c315a63bcf08… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/dev/faq.rst Log Message: ----------- merge... Commit: f7a68ec29567a4dc3067ab0b3bccdc6c32c975d3 https://github.com/galaxyproject/galaxy/commit/f7a68ec29567a4dc3067ab0b3bcc… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M .gitignore M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/hdas.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/workflow/run.py M scripts/common_startup.sh M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-jobs.js.map A static/maps/mvc/upload/upload-row.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-jobs.js A static/scripts/mvc/upload/upload-row.js A test-data/1.RData M test/api/helpers.py M test/api/test_dataset_collections.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/test_data.py M test/base/twilltestcase.py M test/functional/tools/disambiguate_cond.xml M test/functional/tools/min_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/functional/tools/validation_repeat.xml M test/unit/jobs/test_job_configuration.py R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge branch 'dev' of github.com:galaxyproject/galaxy into dev Commit: 2166f876bc938e9837bbb974e24a670e1e12fe98 https://github.com/galaxyproject/galaxy/commit/2166f876bc938e9837bbb974e24a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg M doc/source/index.rst Log Message: ----------- First draft of GIE admin docs Commit: 79c75e6e21aa894c949540160d87f1b7a6c43b39 https://github.com/galaxyproject/galaxy/commit/79c75e6e21aa894c949540160d87… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Added docker-on-another-host Commit: 94c61f9f7f31189f3d7d265cf94fab198f5007b8 https://github.com/galaxyproject/galaxy/commit/94c61f9f7f31189f3d7d265cf94f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Add long tutorial on how-to-GIE Commit: 4b8f9b22a54f828075a7b574762ef0fc19e500dd https://github.com/galaxyproject/galaxy/commit/4b8f9b22a54f828075a7b574762e… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Correct highlighting, and small bugs/typos Commit: 6db64967197b0ee7dff6c4df31d6281c89294720 https://github.com/galaxyproject/galaxy/commit/6db64967197b0ee7dff6c4df31d6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Correct docker_port/proxy_prefix Commit: ed0fefaa4339d8ec96e60c98befa3fa2e5ff07b4 https://github.com/galaxyproject/galaxy/commit/ed0fefaa4339d8ec96e60c98befa… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Full list of env vars, more doc corrections Commit: 928345fad7aa16bd1c32133e9b571954faddd0f3 https://github.com/galaxyproject/galaxy/commit/928345fad7aa16bd1c32133e9b57… Author: Rémi Marenco <remi.marenco(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Fixed the image to show up The .* did not do the trick, added the .png extension so we could see the image. There is still the "interactive_environments_success.png" missing though! If you want me to take the picture, I can. Just need to know exactly what you want to show :p Commit: 98601084ec7f130f0b7dd27354648afd24cb1e78 https://github.com/galaxyproject/galaxy/commit/98601084ec7f130f0b7dd2735464… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge pull request #11 from remimarenco/patch-1 Fixed the interactive_environments' image to show up Commit: 771376a742fc1a248cc2223acebb27f5fd24ba43 https://github.com/galaxyproject/galaxy/commit/771376a742fc1a248cc2223acebb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: A doc/source/admin/interactive_environments_success.png Log Message: ----------- Added success picture Commit: e81517bb9cefb7e4ddab991d3da59ae63619fd81 https://github.com/galaxyproject/galaxy/commit/e81517bb9cefb7e4ddab991d3da5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-26 (Sat, 26 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Merge branch 'gie-docs' of github.com:erasche/galaxy into gie-docs Commit: de03710756c1858b47802bae5b3d3d67fde248b7 https://github.com/galaxyproject/galaxy/commit/de03710756c1858b47802bae5b3d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Comment out default value Commit: 76db6d5274f7fd527d7e161b4ec21492176096f7 https://github.com/galaxyproject/galaxy/commit/76db6d5274f7fd527d7e161b4ec2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Link to the wiki Commit: 86aa3ca22bb820e240642aca64131ff7a5350bd2 https://github.com/galaxyproject/galaxy/commit/86aa3ca22bb820e240642aca6413… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-29 (Tue, 29 Sep 2015) Changed paths: M doc/source/admin/index.rst M doc/source/index.rst Log Message: ----------- Document that this isn't the primary admin docs Commit: d8ce3c25df0e6f0e44278e2dadd771d2030ae087 https://github.com/galaxyproject/galaxy/commit/d8ce3c25df0e6f0e44278e2dadd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A doc/source/admin/index.rst A doc/source/admin/interactive_environments.png A doc/source/admin/interactive_environments.rst A doc/source/admin/interactive_environments.svg A doc/source/admin/interactive_environments_success.png M doc/source/dev/faq.rst M doc/source/index.rst Log Message: ----------- Merge pull request #803 from erasche/gie-docs Document GIEs Compare: https://github.com/galaxyproject/galaxy/compare/c7c269572e61...d8ce3c25df0e

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[galaxyproject/galaxy] 2c45f3: UI, Collections: correct foldout expansion for col...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2c45f356a942a64fb6506358d793bc2c4b4579f9 https://github.com/galaxyproject/galaxy/commit/2c45f356a942a64fb6506358d793… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- UI, Collections: correct foldout expansion for collections only re-rendering on 'populated' or 'visible' change; correct foldout expansion in published histories by giving dataset collection elements an api endpoint and moving 'rerunnable' and 'creating_job' fetch into li-edit Commit: c7c269572e618710b87986b3f4b51d187140dd7e https://github.com/galaxyproject/galaxy/commit/c7c269572e618710b87986b3f4b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-li.js.map M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #819 from carlfeberhard/fix.collection-expansion UI, Collections: correct foldout expansion for collections only re-re… Compare: https://github.com/galaxyproject/galaxy/compare/6ee9a08cf2d3...c7c269572e61

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[galaxyproject/usegalaxy-playbook] e7212a: Test mutable configs
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e7212ad3e22a5d8c50aacec8f06b47294f15f99d https://github.com/galaxyproject/usegalaxy-playbook/commit/e7212ad3e22a5d8c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 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: ----------- Test mutable configs Commit: b4eda1dd56b85084bd43be94df224539bc472575 https://github.com/galaxyproject/usegalaxy-playbook/commit/b4eda1dd56b85084… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M production/group_vars/all.yml M production/group_vars/pulsarservers.yml Log Message: ----------- Update Main Galaxy and Pulsar Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/96d7eadf57b0...…

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[galaxyproject/infrastructure-playbook] bad344: Don't attempt delivery from EC2 via IPv6 since EC2...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: bad3440527eb3dd571d6ad028a5e09c2fb1e6753 https://github.com/galaxyproject/infrastructure-playbook/commit/bad3440527e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M roles/postfix/templates/main.cf.j2 Log Message: ----------- Don't attempt delivery from EC2 via IPv6 since EC2 still doesn't really do IPv6 in a useful way. =(

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[galaxyproject/infrastructure-playbook] 1fafed: Move some athena things over from usegalaxy-playbo...
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1fafed283871b4eaf83747c445af7bbcdc140979 https://github.com/galaxyproject/infrastructure-playbook/commit/1fafed28387… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A galaxyenv/group_vars/ec2hosts.yml A galaxyenv/host_vars/athena.galaxyproject.org.yml M galaxyenv/inventory A galaxyenv/secret_host_vars/athena.galaxyproject.org.yml M roles/postfix/templates/main.cf.j2 Log Message: ----------- Move some athena things over from usegalaxy-playbook. Allow mail relaying through chouffe in the EC2 VPC.

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[galaxyproject/usegalaxy-playbook] 70595d: Moved some athena stuff to infrastructure-playbook
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 70595dbfc1533f3707eca4cc04d9840d308d69af https://github.com/galaxyproject/usegalaxy-playbook/commit/70595dbfc1533f37… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M common/host_vars/athena.galaxyproject.org.yml Log Message: ----------- Moved some athena stuff to infrastructure-playbook Commit: 96d7eadf57b018a016cce4e0932964217510a215 https://github.com/galaxyproject/usegalaxy-playbook/commit/96d7eadf57b018a0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M .gitmodules M README.md M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py A files/galaxy/common/static/welcome_img/GCC2016TrNom.png A files/galaxy/common/static/welcome_img/Riboseq.png A files/galaxy/common/static/welcome_img/WhaleSharkGalaxy.png M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml M files/galaxy/test.galaxyproject.org/config/tool_conf.xml R files/galaxy/test.galaxyproject.org/dynamic_rules/blacklight_select.py A files/galaxy/test.galaxyproject.org/dynamic_rules/greenfield_select.py R files/galaxy/test.galaxyproject.org/nagios/echo_test_blacklight.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_greenfield.xml A files/galaxy/test.galaxyproject.org/tool_list.yaml 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 A files/galaxy/usegalaxy.org/tool_list.yaml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M galaxy.yml M production/group_vars/all.yml M production/group_vars/galaxyservers.yml M production/group_vars/pulsarservers.yml M production/group_vars/toolshedservers.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml A production/secret_host_vars/default.yml A production/secret_host_vars/login5.stampede.tacc.utexas.edu.yml M production/secret_vars/galaxyservers.yml R production/secret_vars/pulsarservers.yml M pulsar.yml M roles/galaxyprojectdotorg.pulsar/README.md M roles/galaxyprojectdotorg.pulsar/defaults/main.yml M roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info M roles/galaxyprojectdotorg.pulsar/tasks/main.yml A roles/galaxyprojectdotorg.pulsar/templates/app.yml.j2 M roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 A roles/galaxyprojectdotorg.tools/LICENSE A roles/galaxyprojectdotorg.tools/README.md A roles/galaxyprojectdotorg.tools/defaults/main.yml A roles/galaxyprojectdotorg.tools/files/README.md A roles/galaxyprojectdotorg.tools/files/dbkeys_list.yaml.sample A roles/galaxyprojectdotorg.tools/files/install_tool_shed_tools.py A roles/galaxyprojectdotorg.tools/files/tool_list.yaml A roles/galaxyprojectdotorg.tools/files/tool_list.yaml.sample A roles/galaxyprojectdotorg.tools/meta/.galaxy_install_info A roles/galaxyprojectdotorg.tools/meta/main.yml A roles/galaxyprojectdotorg.tools/tasks/main.yml A roles/galaxyprojectdotorg.tools/tasks/tools.yml M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/pulsarservers.yml M stage/group_vars/toolshedservers.yml A stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml R stage/host_vars/tg-login2.blacklight.psc.xsede.org.yml M stage/inventory A stage/secret_host_vars/default.yml A stage/secret_host_vars/greenfield.psc.xsede.org.yml A stage/secret_host_vars/login5.stampede.tacc.utexas.edu.yml M stage/secret_vars/galaxyservers.yml R stage/secret_vars/pulsarservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 A tools.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/85d58d667cd5...…

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[galaxyproject/infrastructure-playbook] 0ae54c: Update ssh key
by GitHub 30 Sep '15

30 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0ae54c6d19e0667c51e519aafd4fd6b18707d69e https://github.com/galaxyproject/infrastructure-playbook/commit/0ae54c6d19e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Update ssh key Commit: 3f481bca5fd7b351253324f21fe9581320aafdfb https://github.com/galaxyproject/infrastructure-playbook/commit/3f481bca5fd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-30 (Wed, 30 Sep 2015) Changed paths: A galaxyenv/group_vars/jenkinsservers.yml M galaxyenv/host_vars/n2.galaxyproject.org.yml M playbook.yml A roles/linuxbrew/defaults/main.yml A roles/linuxbrew/tasks/main.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/be07399e8d…

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