galaxy-commits April 2017

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[galaxyproject/galaxy] 8e0be5: [17.01] Fix collection operations in workflows.
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 8e0be5089c63d94b841babfffcd70f2d8ab9b27c https://github.com/galaxyproject/galaxy/commit/8e0be5089c63d94b841babfffcd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-03 (Mon, 03 Apr 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- [17.01] Fix collection operations in workflows. Due to a couple bugs things weren't being delayed correctly for some of these tools in some workflows. Commit: 7e4f805d479acc8f362ed651330f91fb8e2c9c40 https://github.com/galaxyproject/galaxy/commit/7e4f805d479acc8f362ed651330f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/execute.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #3848 from jmchilton/collection_operation_check_inputs_bug [17.01] Fix collection operations in workflows. Compare: https://github.com/galaxyproject/galaxy/compare/352a4920a93f...7e4f805d479a

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[galaxyproject/galaxy] 388bb4: Stats docs
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 388bb42ba067a1464c1393208c3d6eea7eff0315 https://github.com/galaxyproject/galaxy/commit/388bb42ba067a1464c1393208c3d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- Stats docs Commit: 45e40a184a416e28d771c3cca4f487b06b6e284e https://github.com/galaxyproject/galaxy/commit/45e40a184a416e28d771c3cca4f4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: A doc/source/admin/special_topics/grafana.png M doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst Log Message: ----------- Merge pull request #3968 from erasche/stats-docs Stats docs Compare: https://github.com/galaxyproject/galaxy/compare/b9effa4a2b7c...45e40a184a41

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[galaxyproject/galaxy] c9087f: Graphite support
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c9087fe21e650892af647940915f3bcfbac693cc https://github.com/galaxyproject/galaxy/commit/c9087fe21e650892af647940915f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Graphite support Commit: 26c06880c2d49bda0c03c0ec11f39e6a529a962b https://github.com/galaxyproject/galaxy/commit/26c06880c2d49bda0c03c0ec11f3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- flake8 Commit: b9effa4a2b7ccad8e210243853d0e9429b3b034d https://github.com/galaxyproject/galaxy/commit/b9effa4a2b7ccad8e210243853d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt A lib/galaxy/web/framework/middleware/graphite.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #3964 from erasche/graphite Graphite support Compare: https://github.com/galaxyproject/galaxy/compare/57c4020518f0...b9effa4a2b7c

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[galaxyproject/galaxy] 908dd2: Fix some typos in config/galaxy.ini.sample
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 908dd2d342bbd5467b52211ba6fcbf02788d2371 https://github.com/galaxyproject/galaxy/commit/908dd2d342bbd5467b52211ba6fc… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Fix some typos in config/galaxy.ini.sample Commit: 57c4020518f05221c118c9254111f789f4fe2116 https://github.com/galaxyproject/galaxy/commit/57c4020518f05221c118c9254111… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3971 from nsoranzo/galaxy.ini_typos Fix some typos in config/galaxy.ini.sample Compare: https://github.com/galaxyproject/galaxy/compare/2b05fd050a3e...57c4020518f0

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[galaxyproject/galaxy] ade550: Fix some selectors in tours
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ade550f9527fd1651d79a9d01f1a4dc798585bcf https://github.com/galaxyproject/galaxy/commit/ade550f9527fd1651d79a9d01f1a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Fix some selectors in tours Commit: 898f22c75d5a0afeeb30df113f304e66a5b4c70b https://github.com/galaxyproject/galaxy/commit/898f22c75d5a0afeeb30df113f30… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.history.yaml Log Message: ----------- More fixes for History Intro tour - Remove unnecessary quotes that end up in the pop-up - Fix one pop-up title - Remove one step that is broken if the user is already logged-in Commit: feb31685f63f6805d2e5953697b9ed531a44379d https://github.com/galaxyproject/galaxy/commit/feb31685f63f6805d2e5953697b9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml Log Message: ----------- Do not click on the section name, it is already expanded Introduced in commit ca36c0dbfd438708e35e18d06c603f2cc2ce7047 . Commit: 2b05fd050a3e1b517ca992a37f5d574521a37dd2 https://github.com/galaxyproject/galaxy/commit/2b05fd050a3e1b517ca992a37f5d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml Log Message: ----------- Merge pull request #3970 from nsoranzo/tour_fixes Tour fixes Compare: https://github.com/galaxyproject/galaxy/compare/060dc7379e4a...2b05fd050a3e

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[galaxyproject/galaxy] eb6ebc: Fix JJ's column_join tool depending on Galaxy at r...
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eb6ebc72ea6abd0cc2f497d57872b261456b9e4b https://github.com/galaxyproject/galaxy/commit/eb6ebc72ea6abd0cc2f497d57872… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix JJ's column_join tool depending on Galaxy at runtime. https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=e752a5a291d2… Commit: 352a4920a93f6c92c4713e6f0b118f3ffe31997e https://github.com/galaxyproject/galaxy/commit/352a4920a93f6c92c4713e6f0b11… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3961 from jmchilton/another_legacy_fix [17.01] Fix JJ's column_join tool depending on Galaxy at runtime. Commit: 060dc7379e4a74c33a19e82c6a160f97bab1cf9e https://github.com/galaxyproject/galaxy/commit/060dc7379e4a74c33a19e82c6a16… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_17.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/aa024f6d2338...060dc7379e4a

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[galaxyproject/usegalaxy-playbook] 359fee: Install Conda locally on Jetstream
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 359fee70192fd94fe8c2b505e77e94909f7f7bbf https://github.com/galaxyproject/usegalaxy-playbook/commit/359fee70192fd94f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: R env/common/files/pulsar/config/jetstream_dependency_resolvers_conf.xml A env/common/templates/pulsar/config/jetstream_dependency_resolvers_conf.xml.j2 M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/test/templates/pulsar Log Message: ----------- Install Conda locally on Jetstream

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[galaxyproject/usegalaxy-playbook] f5c031: Upgrade Main Pulsar
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f5c0310b009c6bf2f94335486d753c1a2bc6aa33 https://github.com/galaxyproject/usegalaxy-playbook/commit/f5c0310b009c6bf2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M production/group_vars/pulsarservers.yml Log Message: ----------- Upgrade Main Pulsar Commit: 9c8d4734f98ae8731096cbe9bf96f5b379fcc15f https://github.com/galaxyproject/usegalaxy-playbook/commit/9c8d4734f98ae873… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: R files/pulsar/usegalaxy.org/config/jetstream_dependency_resolvers_conf.xml M production/host_vars/jetstream-iu0.galaxyproject.org.yml M production/host_vars/jetstream-tacc0.galaxyproject.org.yml A templates/pulsar/usegalaxy.org/config/jetstream_dependency_resolvers_conf.x… Log Message: ----------- Install Conda locally on Jetstream Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/448253e6cd22...…

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[galaxyproject/galaxy] eb6ebc: Fix JJ's column_join tool depending on Galaxy at r...
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: eb6ebc72ea6abd0cc2f497d57872b261456b9e4b https://github.com/galaxyproject/galaxy/commit/eb6ebc72ea6abd0cc2f497d57872… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix JJ's column_join tool depending on Galaxy at runtime. https://toolshed.g2.bx.psu.edu/repository/browse_repository?id=e752a5a291d2… Commit: 352a4920a93f6c92c4713e6f0b118f3ffe31997e https://github.com/galaxyproject/galaxy/commit/352a4920a93f6c92c4713e6f0b11… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3961 from jmchilton/another_legacy_fix [17.01] Fix JJ's column_join tool depending on Galaxy at runtime. Compare: https://github.com/galaxyproject/galaxy/compare/1fe9c4d066e1...352a4920a93f

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[galaxyproject/galaxy] 9c44ae: Followup to exception refactoring, fixes a few iss...
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c44ae01cd99e8d23335bbf5846d1a777b777969 https://github.com/galaxyproject/galaxy/commit/9c44ae01cd99e8d23335bbf5846d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_registry.py Log Message: ----------- Followup to exception refactoring, fixes a few issues @nsoranzo noticed with my semiautomatic refactorings. Commit: 0bd59518a6411858a44f1fe5a4bd8082df74353d https://github.com/galaxyproject/galaxy/commit/0bd59518a6411858a44f1fe5a4bd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Unused exception, templates. Commit: aa024f6d23389dd8868ce85f7544f1c7b3f58a8e https://github.com/galaxyproject/galaxy/commit/aa024f6d23389dd8868ce85f7544… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/repository_registry.py Log Message: ----------- Merge pull request #3959 from dannon/exception_refactor_tweaks Followup to exception refactoring Compare: https://github.com/galaxyproject/galaxy/compare/e842a2658759...aa024f6d2338

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galaxy-commits April 2017