- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 779156: add two tools from str_fm repository to galaxy mod...
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 779156111a117f5513ae10af04d0b12052627a32 https://github.com/galaxyproject/galaxy/commit/779156111a117f5513ae10af04d0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- add two tools from str_fm repository to galaxy module whitelist we broke them so we are fixing it Commit: 1d0ace1452aa9d5e334ee89aca07fa401db37806 https://github.com/galaxyproject/galaxy/commit/1d0ace1452aa9d5e334ee89aca07… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3973 from martenson/strfm-fix [17.01] add two tools from str_fm repository to galaxy module whitelist Compare: https://github.com/galaxyproject/galaxy/compare/02bdc7495d80...1d0ace1452aa

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[galaxyproject/infrastructure-playbook] e414b1: Add Jenkins/Github integration
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e414b165cd9b4a3fa99979955c11354d3f65a2c7 https://github.com/galaxyproject/infrastructure-playbook/commit/e414b165cd9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M galaxyenv/files/jenkins/jenkins_server_user_ssh_config M galaxyenv/files/jenkins/jenkins_slave_user_ssh_config M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_group_vars/jenkinsslaves.yml Log Message: ----------- Add Jenkins/Github integration

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[galaxyproject/galaxy] d41ad5: Fix margin style values for color picker element
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d41ad577617da2577b5dabadb47cb37a7edc5cb1 https://github.com/galaxyproject/galaxy/commit/d41ad577617da2577b5dabadb47c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix margin style values for color picker element Commit: a6a920cb5ebb71a8f0349e733b31ffdd70ffab27 https://github.com/galaxyproject/galaxy/commit/a6a920cb5ebb71a8f0349e733b31… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/style/blue/base.css Log Message: ----------- Remove unused label attribute, fix styles within color selector, remove encoded style attributes Commit: 9aa7c6d2e905fc83bb9aee2c06f85f6aa7e1ad8c https://github.com/galaxyproject/galaxy/commit/9aa7c6d2e905fc83bb9aee2c06f8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js 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 M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge branch 'dev' into fix_color_input_style Commit: 722c294165eb40aad9d8f4a3d02e383563064b3e https://github.com/galaxyproject/galaxy/commit/722c294165eb40aad9d8f4a3d02e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Use first/last child selector Commit: 6c51f5232a7af4b0a73d803b4a3e7c64b23ec9c7 https://github.com/galaxyproject/galaxy/commit/6c51f5232a7af4b0a73d803b4a3e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-color-picker.js Log Message: ----------- Remove unused classes from code file Commit: 399c7f061ceff36c355536abd499362edc6f90d5 https://github.com/galaxyproject/galaxy/commit/399c7f061ceff36c355536abd499… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/style/less/ui.less M static/maps/mvc/ui/ui-color-picker.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-color-picker.js M static/style/blue/base.css Log Message: ----------- Merge pull request #3965 from guerler/fix_color_input_style Fix margin style values for color picker element Compare: https://github.com/galaxyproject/galaxy/compare/45e40a184a41...399c7f061cef

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[galaxyproject/galaxy] 923442: Fix multiple collection reductions on multiple dat...
by GitHub 25 Apr '17

25 Apr '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 9234420cd770661b58ee91051015e9580505ca47 https://github.com/galaxyproject/galaxy/commit/9234420cd770661b58ee91051015… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-05 (Wed, 05 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M test/qunit/tests/ui_tests.js Log Message: ----------- Fix multiple collection reductions on multiple data parameters. Was introduced in #805 but there was a small bug (maybe a last minute change before opening the PR) in the client code so this never was exposed to the users the way it was intended. This should largely negate the need for hacks such as in cuffmerge that allow multiple list collections in addition to main multiple data selector. xref galaxyproject/tools-iuc#1225. Commit: 02bdc7495d80d4fb085de26e07e200a95a20ec56 https://github.com/galaxyproject/galaxy/commit/02bdc7495d80d4fb085de26e07e2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M static/maps/mvc/ui/ui-select-content.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-select-content.js M test/qunit/tests/ui_tests.js Log Message: ----------- Merge pull request #3875 from jmchilton/fix_multi_collection_multi_data_param_reductions [17.01] Fix multiple collection reductions on multiple data parameters. Compare: https://github.com/galaxyproject/galaxy/compare/7e4f805d479a...02bdc7495d80

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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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[galaxyproject/infrastructure-playbook] 2db848: Create symlinks for conda dep resolution in Pulsar
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2db8485a502ab6574f50301f62b14a2995563cb2 https://github.com/galaxyproject/infrastructure-playbook/commit/2db8485a502… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M jetstreamiuenv/group_vars/controllers.yml M jetstreamtaccenv/group_vars/controllers.yml Log Message: ----------- Create symlinks for conda dep resolution in Pulsar

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[galaxyproject/infrastructure-playbook] 4c22d7: Update GIE Docker image volume
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4c22d7e9f1d98bf8e734440cef30ad5cfe093c51 https://github.com/galaxyproject/infrastructure-playbook/commit/4c22d7e9f1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M jetstreamdockerenv/group_vars/imageinstances.yml Log Message: ----------- Update GIE Docker image volume

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[galaxyproject/usegalaxy-playbook] 448253: Enable Conda on Main Jetstream
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 448253e6cd22b4ac0bba5266aec3d4a376374810 https://github.com/galaxyproject/usegalaxy-playbook/commit/448253e6cd22b4ac… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A 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 Log Message: ----------- Enable Conda on Main Jetstream

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[galaxyproject/usegalaxy-playbook] 9ff176: Use Conda on Jetstream
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9ff176d1b0f074e93da2055e29b6decd16b09ead https://github.com/galaxyproject/usegalaxy-playbook/commit/9ff176d1b0f074e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: A env/common/files/pulsar/config/jetstream_dependency_resolvers_conf.xml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml Log Message: ----------- Use Conda on Jetstream

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[galaxyproject/galaxy] 0fc0a4: change 'user' menu to login or register for anons
by GitHub 24 Apr '17

24 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0fc0a49b4bb7de0f95bdd8f594a22515243cd4a7 https://github.com/galaxyproject/galaxy/commit/0fc0a49b4bb7de0f95bdd8f594a2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- change 'user' menu to login or register for anons Commit: 1fa8c837accda3d8120538da98ef200ab0250453 https://github.com/galaxyproject/galaxy/commit/1fa8c837accda3d8120538da98ef… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- improve french localization of the new menu item Commit: e842a265875909a0bead4e6e3e9f8006170067c3 https://github.com/galaxyproject/galaxy/commit/e842a265875909a0bead4e6e3e9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-24 (Mon, 24 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map M static/maps/nls/fr/locale.js.map M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merge pull request #3955 from martenson/user-menu-ux change 'user' menu to login or register for anons Compare: https://github.com/galaxyproject/galaxy/compare/439579298acb...e842a2658759

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[galaxyproject/galaxy] 33d662: Fix another tool (GeneBed_Maf_Fasta2) requiring th...
by GitHub 21 Apr '17

21 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33d6628dabdf75c27979925cb45b94e7ab59d725 https://github.com/galaxyproject/galaxy/commit/33d6628dabdf75c27979925cb45b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Commit: 1fe9c4d066e11b61767e22475a1392e0bbacf196 https://github.com/galaxyproject/galaxy/commit/1fe9c4d066e11b61767e22475a13… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3931 from jmchilton/maf_fix_47 [17.01] Fix another tool (GeneBed_Maf_Fasta2) requiring the legacy Galaxy environment. Commit: 439579298acbe2f85d79dd484ba1dca9cb15eee3 https://github.com/galaxyproject/galaxy/commit/439579298acbe2f85d79dd484ba1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #3956 from galaxyproject/release_17.01 merge Release 17.01 Compare: https://github.com/galaxyproject/galaxy/compare/e04ac6100378...439579298acb

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[galaxyproject/galaxy] 4adda2: Remove Google from OpenID providers in the sample....
by GitHub 21 Apr '17

21 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4adda20b0b75ba68ebc69b4aefc86adea68299d4 https://github.com/galaxyproject/galaxy/commit/4adda20b0b75ba68ebc69b4aefc8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/openid_conf.xml.sample R openid/google.xml Log Message: ----------- Remove Google from OpenID providers in the sample. Google dropped OpenID support a while back. Commit: 0bc8d1f4ceb8bf3a212c5d17ddc2a1aa3e096191 https://github.com/galaxyproject/galaxy/commit/0bc8d1f4ceb8bf3a212c5d17ddc2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M config/openid_conf.xml.sample Log Message: ----------- move genomespace as the first shown provider in selection Commit: e04ac61003787ea7c99bc524017ae8afaec1decf https://github.com/galaxyproject/galaxy/commit/e04ac61003787ea7c99bc524017a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M config/openid_conf.xml.sample R openid/google.xml Log Message: ----------- Merge pull request #3953 from dannon/openid_sample_nogoogle Remove Google from OpenID providers in the sample. Compare: https://github.com/galaxyproject/galaxy/compare/386afbb4f6ac...e04ac6100378

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[galaxyproject/galaxy] 8599df: Standardize usage of log.exception in datatypes re...
by GitHub 21 Apr '17

21 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8599dff7a0098e121ddb244345a1c478f0a05cee https://github.com/galaxyproject/galaxy/commit/8599dff7a0098e121ddb244345a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Standardize usage of log.exception in datatypes registry. Commit: d303cf5ffbea29ad9d0d96b167f20606a022a488 https://github.com/galaxyproject/galaxy/commit/d303cf5ffbea29ad9d0d96b167f2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py Log Message: ----------- Strip exception strings from being included in log.exception statements across the project. Commit: c46e36bdee354a879d2770b0ec9e22b00ec1c104 https://github.com/galaxyproject/galaxy/commit/c46e36bdee354a879d2770b0ec9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Overhaul string templating in log.exception statements -- should apply to all logs, eventually. Commit: d43d7aa140f399fbaa65308fe842c9afba8c44a3 https://github.com/galaxyproject/galaxy/commit/d43d7aa140f399fbaa65308fe842… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-04-14 (Fri, 14 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Fix E241, F841 from exception refactoring. Commit: 386afbb4f6ac703c60d2ffd975a1c3740f67457b https://github.com/galaxyproject/galaxy/commit/386afbb4f6ac703c60d2ffd975a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-21 (Fri, 21 Apr 2017) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/local.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/tasks.py M lib/galaxy/managers/citations.py M lib/galaxy/model/migrate/versions/0048_dataset_instance_state_column.py M lib/galaxy/model/migrate/versions/0062_user_openid_table.py M lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py M lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py M lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py M lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py M lib/galaxy/model/migrate/versions/0119_job_metrics.py M lib/galaxy/model/migrate/versions/0120_dataset_collections.py M lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py M lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py M lib/galaxy/model/migrate/versions/0124_job_state_history.py M lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py M lib/galaxy/model/migrate/versions/0126_password_reset.py M lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py M lib/galaxy/model/migrate/versions/0128_session_timeout.py M lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py M lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py M lib/galaxy/model/migrate/versions/0134_hda_set_deleted_if_purged.py M lib/galaxy/queue_worker.py M lib/galaxy/sample_tracking/external_service_types.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/verify/asserts/__init__.py M lib/galaxy/tours/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/visualization/genomes.py M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/galaxy_install/tools/data_manager.py M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/repository_registry.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/workflow_util.py M lib/tool_shed/utility_containers/__init__.py Log Message: ----------- Merge pull request #3933 from dannon/exception_logging_fixes Standardize usage of log.exception Compare: https://github.com/galaxyproject/galaxy/compare/01b3eb42d88b...386afbb4f6ac

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[galaxyproject/galaxy] 9b6a9d: Start work on a relabelling collection operation.
by GitHub 20 Apr '17

20 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff https://github.com/galaxyproject/galaxy/commit/9b6a9dc0c73dfc0625e55a3db4c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_1.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Start work on a relabelling collection operation. I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is: - Validate uniqueness of identifiers and provide nice messages if they are not unique. - Validate that at least the required number of lines are present in the file and provide a nice message if not. - Add strict mode to ensure exactly the correct number of lines is added. - Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created. - Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration. - Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool. Commit: d21c14f0096b1fa7954396e7e9878b1d1e712331 https://github.com/galaxyproject/galaxy/commit/d21c14f0096b1fa7954396e7e987… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_2.txt Log Message: ----------- Add possibility to rename collection items from a tabular file Commit: 338130a979c99f60a171ba6b9ffca5db0a0e16a8 https://github.com/galaxyproject/galaxy/commit/338130a979c99f60a171ba6b9ffc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Fix failing test case in relable_from_file based on comment from @mvdbeek. Commit: 09bcdd9185e969c0eec34770faf8cb418c0f3e47 https://github.com/galaxyproject/galaxy/commit/09bcdd9185e969c0eec34770faf8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-13 (Thu, 13 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_1.txt Log Message: ----------- Various improvements to relabel from file collection operation. - Better error handling (check for bad characters when creating collections). - Implement a strict mode parameter to do even more validation. - Rework tabular vs txt mode to be explicit user choice. - Mirror fix in release_17.01 for datasets not having a history, Commit: 2288a88ab793198147fdb5a1050d0325a831d9f8 https://github.com/galaxyproject/galaxy/commit/2288a88ab793198147fdb5a1050d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml A test-data/new_labels_bad_2.txt Log Message: ----------- Fix relabel_from_file collection operation error handling if duplicate identifiers. Commit: 49abfced0918e2722ad0325aa7df6abbd2c5019e https://github.com/galaxyproject/galaxy/commit/49abfced0918e2722ad0325aa7df… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml M lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement collection operation for filtering lists from a file. Commit: 01b3eb42d88b1900b73a8dfb9eecdbce49e531e0 https://github.com/galaxyproject/galaxy/commit/01b3eb42d88b1900b73a8dfb9eec… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_from_file.xml A lib/galaxy/tools/relabel_from_file.xml A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3940 from jmchilton/collection_op_filter_from_file Collection Operation - Filtering from a File Compare: https://github.com/galaxyproject/galaxy/compare/9f4fd7c44964...01b3eb42d88b

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[galaxyproject/galaxy] abe643: Update ethercalc GIE for readiness checking
by GitHub 20 Apr '17

20 Apr '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: abe6434916812a8236052560d58ab184b98b3ccb https://github.com/galaxyproject/galaxy/commit/abe6434916812a8236052560d58a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako Log Message: ----------- Update ethercalc GIE for readiness checking Commit: a2b8b43179cbf880f1e16ab43172545e4309c058 https://github.com/galaxyproject/galaxy/commit/a2b8b43179cbf880f1e16ab43172… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Generate proper url for readiness endpoint Commit: 154530994f979070fe8c94c7730a99d11164c7fc https://github.com/galaxyproject/galaxy/commit/154530994f979070fe8c94c7730a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Error handling for GIE container readiness check Commit: 1e536e4ec7325b8d61394ea4091d8285eff24315 https://github.com/galaxyproject/galaxy/commit/1e536e4ec7325b8d61394ea4091d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-17 (Mon, 17 Apr 2017) Changed paths: M config/containers_conf.yml.sample M lib/galaxy/containers/docker_swarm.py Log Message: ----------- Add an ignore_volumes option for swarm_mode containers Commit: 9f4fd7c449646f8c3da9ba90d642a99b9cec386c https://github.com/galaxyproject/galaxy/commit/9f4fd7c449646f8c3da9ba90d642… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/containers_conf.yml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M lib/galaxy/containers/docker_swarm.py M static/maps/galaxy.interactive_environments.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.interactive_environments.js Log Message: ----------- Merge pull request #3941 from natefoo/containers-bugfixes Containers interface and GIE bugfixes Compare: https://github.com/galaxyproject/galaxy/compare/e9011488f2f5...9f4fd7c44964

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[galaxyproject/usegalaxy-playbook] 89fb31: Main mutable config updates
by GitHub 19 Apr '17

19 Apr '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 89fb31b48a37fd54891c99eb4117dbcf8d2d3dbe https://github.com/galaxyproject/usegalaxy-playbook/commit/89fb31b48a37fd54… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-04-19 (Wed, 19 Apr 2017) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable config updates

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