February 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c7b6af: Add a script for dumping library file paths for ba...
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c7b6afbcd25fdeef9d7a59df95e3ace3136e0fa9 https://github.com/galaxyproject/galaxy/commit/c7b6afbcd25fdeef9d7a59df95e3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: A scripts/dump_library_paths.py Log Message: ----------- Add a script for dumping library file paths for backup Commit: 5a31ac84ce129d03aea5fcbd73edaa4d67c465e5 https://github.com/galaxyproject/galaxy/commit/5a31ac84ce129d03aea5fcbd73ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: A scripts/dump_library_paths.py Log Message: ----------- Merge pull request #5436 from natefoo/dump-library-paths A script for dumping library file paths for backup Compare: https://github.com/galaxyproject/galaxy/compare/b1df43a1f83a...5a31ac84ce12

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[galaxyproject/galaxy] 7490fd: More robust nametag discovery and propagation.
by GitHub 02 Feb '18

02 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7490fd452046b4a4578f6401501439773cbf2f28 https://github.com/galaxyproject/galaxy/commit/7490fd452046b4a4578f64015014… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- More robust nametag discovery and propagation. - Nametags weren't being picked up on collection inputs - so for instance tools that take in a single collection and produce a dataset or file weren't propagating nametags (unless the collection contents had tags). To see this create two unnamed datasets without tags, create a pair from them, add a tag to the pair, and run the pair through the "paired_test" test tool. - Nametags weren't being propagated to the outputs of collection operations. Commit: 6f40f7098d507895c6c6608aff6a698289f2eeb6 https://github.com/galaxyproject/galaxy/commit/6f40f7098d507895c6c6608aff6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Cleanup collection operation tagging implementation thanks to @mvdbeek comments. Commit: 6022fe7d7e90b0da0cad83589d5d630f6dd1d386 https://github.com/galaxyproject/galaxy/commit/6022fe7d7e90b0da0cad83589d5d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle optional inputs when collecting preserved tags. https://github.com/galaxyproject/galaxy/pull/5403/files#r165283450 Commit: 60561c20307cf0585e553d0fa5cd612716ab7975 https://github.com/galaxyproject/galaxy/commit/60561c20307cf0585e553d0fa5cd… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-02 (Fri, 02 Feb 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/model_operations.py Log Message: ----------- Merge pull request #5403 from jmchilton/collection_operation_tags [18.01] More robust nametag discovery and propagation. Compare: https://github.com/galaxyproject/galaxy/compare/f24043e8a74e...60561c20307c

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[galaxyproject/usegalaxy-playbook] 0a1fad: Update TTS
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0a1fada824cfa1e26991b9a6adeac5db27590915 https://github.com/galaxyproject/usegalaxy-playbook/commit/0a1fada824cfa1e2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update TTS

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[galaxyproject/galaxy] 6d8edc: Admin doc corrections
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6d8edce33157e81112889ae7f241903747da3c92 https://github.com/galaxyproject/galaxy/commit/6d8edce33157e81112889ae7f241… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Admin doc corrections Commit: f24043e8a74e3cb2070b06652d9a72be46e6a278 https://github.com/galaxyproject/galaxy/commit/f24043e8a74e3cb2070b06652d9a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 [18.01] Admin doc corrections Compare: https://github.com/galaxyproject/galaxy/compare/ffaabe0a63f4...f24043e8a74e

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[galaxyproject/galaxy] a1662e: remove lib/galaxy/dependencies/conda-environment.t...
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a1662e37059e6956cdca3cb3eb235fd7b890b5c4 https://github.com/galaxyproject/galaxy/commit/a1662e37059e6956cdca3cb3eb23… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: R lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- remove lib/galaxy/dependencies/conda-environment.txt the file is no longer valid and has been replaced by conda-file.sh I believe Commit: b1df43a1f83a2b3026e23758843017d428e56a64 https://github.com/galaxyproject/galaxy/commit/b1df43a1f83a2b3026e237588430… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: R lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #5440 from martenson/remove-condaenv-txt remove lib/galaxy/dependencies/conda-environment.txt Compare: https://github.com/galaxyproject/galaxy/compare/b4cdce925bf4...b1df43a1f83a

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[galaxyproject/infrastructure-playbook] 8b1d72: Automatically balance normal/multi partitions on r...
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8b1d7203ee90d92a15d8f6b6fba2e26f6b8a546e https://github.com/galaxyproject/infrastructure-playbook/commit/8b1d7203ee9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: A taccenv/files/slurm/spartbalance A taccenv/group_vars/slurmservers.yml Log Message: ----------- Automatically balance normal/multi partitions on roundup to try to avoid waiting normal jobs.

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[galaxyproject/galaxy] 6bdd75: WIP framework dependencies doc update
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6bdd755aafbb008422db46231949ad3c6e4e608f https://github.com/galaxyproject/galaxy/commit/6bdd755aafbb008422db46231949… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- WIP framework dependencies doc update Commit: fd96864bd6fca8f4ff149ca0ba270ebb164254ac https://github.com/galaxyproject/galaxy/commit/fd96864bd6fca8f4ff149ca0ba27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Finish updates to framework dependencies doc Commit: 6333e83a6517830599d17e42707f0bead367d135 https://github.com/galaxyproject/galaxy/commit/6333e83a6517830599d17e42707f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Doc corrections from @nsoranzo Commit: 6070bf07e18b0d3ebc210f3c4c44a1ed14b1dd27 https://github.com/galaxyproject/galaxy/commit/6070bf07e18b0d3ebc210f3c4c44… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css Log Message: ----------- simplify Webhooks' structure Commit: ada76931d8231a83ff15667ccec652b06bd793d4 https://github.com/galaxyproject/galaxy/commit/ada76931d8231a83ff15667ccec6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M lib/galaxy/webhooks/__init__.py Log Message: ----------- add weighted random webhook pick Commit: 90d59ac9234d7a756eb3040cccb35c6e181826ec https://github.com/galaxyproject/galaxy/commit/90d59ac9234d7a756eb3040cccb3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M test/api/test_webhooks.py M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- fix webhooks tests Commit: 57c1fc78043220ec16081255c2b15e854cac976c https://github.com/galaxyproject/galaxy/commit/57c1fc78043220ec16081255c2b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js Log Message: ----------- Client formatting of webhooks changes. Commit: 0ac7b7830dd06ef474002a57c677ca429913d766 https://github.com/galaxyproject/galaxy/commit/0ac7b7830dd06ef474002a57c677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix import order in webhooks/__init__.py Commit: 3b7daece0460286288a8678c5020dd6530d5457f https://github.com/galaxyproject/galaxy/commit/3b7daece0460286288a8678c5020… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/webhooks.js Log Message: ----------- Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported. Commit: 22b0b2f2e90249feacacd0f8cfb60a9335bb40e9 https://github.com/galaxyproject/galaxy/commit/22b0b2f2e90249feacacd0f8cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/qunit/tests/page_tests.js Log Message: ----------- Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes. Commit: fa0ba22f97cbf69c30828205ea94358094b654e0 https://github.com/galaxyproject/galaxy/commit/fa0ba22f97cbf69c30828205ea94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix webhook filtering, make it a bit more defensive. Minor other tweaks. Commit: 9b4465efd37fe7c27276971a2348283e41cc9027 https://github.com/galaxyproject/galaxy/commit/9b4465efd37fe7c27276971a2348… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- fix webhook's property name Commit: 29c766167a64f302341101b0a7301fcd29634698 https://github.com/galaxyproject/galaxy/commit/29c766167a64f302341101b0a730… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- update webhooks docs Commit: a37b638491bc1d04be266bf9a14852fcfb62c342 https://github.com/galaxyproject/galaxy/commit/a37b638491bc1d04be266bf9a148… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #5390 from natefoo/framework-dependencies-doc-update [18.01] Update framework dependencies documentation Commit: ffaabe0a63f47c57cd9785de84cf9e77e398b95c https://github.com/galaxyproject/galaxy/commit/ffaabe0a63f47c57cd9785de84cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge pull request #5342 from dannon/integration.webhooks_improvements [18.01] Webhooks improvements Commit: b4cdce925bf485ecdb24868bacdcffe2f4e7a717 https://github.com/galaxyproject/galaxy/commit/b4cdce925bf485ecdb24868bacdc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md M doc/source/admin/special_topics/webhooks.rst A lib/galaxy/dependencies/conda-file.sh M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M scripts/common_startup.sh M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge branch 'release_18.01' into dev I removed the conflicted file that was modified in dev after removal in 18.01 Compare: https://github.com/galaxyproject/galaxy/compare/a76614486be3...b4cdce925bf4

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[galaxyproject/usegalaxy-playbook] db03a5: More mutable configs
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: db03a5e84cfde3cc40a7682fe273477ffd28e558 https://github.com/galaxyproject/usegalaxy-playbook/commit/db03a5e84cfde3cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- More mutable configs

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[galaxyproject/usegalaxy-playbook] 67ad45: Set slow log threshold correctly
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 67ad4503c6c4bc15c0a5a775203a9b08fd9eaeb1 https://github.com/galaxyproject/usegalaxy-playbook/commit/67ad4503c6c4bc15… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Set slow log threshold correctly Commit: 76c3ef26730370ec44b808964e9d85cae6b15c87 https://github.com/galaxyproject/usegalaxy-playbook/commit/76c3ef26730370ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b68ea53bac01...…

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[galaxyproject/usegalaxy-playbook] 173e0b: Attempt to log queries on Test slower than 1s
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 173e0b72b56cd125481012d86fb7efe9ac79ac58 https://github.com/galaxyproject/usegalaxy-playbook/commit/173e0b72b56cd125… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Attempt to log queries on Test slower than 1s Commit: 02e5f3474715cf2887e187ab832159de558fdd40 https://github.com/galaxyproject/usegalaxy-playbook/commit/02e5f3474715cf28… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run IUC Trinity on Bridges. Commit: b68ea53bac010a37a4091a8ee3076bdeec27d71c https://github.com/galaxyproject/usegalaxy-playbook/commit/b68ea53bac010a37… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M CHANGELOG.md M env/common/files/pulsar/config/bridges_dependency_resolvers_conf.xml Log Message: ----------- More Bridges fixes for Trinity. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2f5e366ffe6f...…

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