October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 42dc7b: Filter histories for visualization grids by user
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 42dc7b361756b096f9d3b17c06e2db1a5cefbe61 https://github.com/galaxyproject/galaxy/commit/42dc7b361756b096f9d3b17c06e2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Filter histories for visualization grids by user Commit: 799fda61dbf3ddaad1b386d9d32602ef2b1c8a83 https://github.com/galaxyproject/galaxy/commit/799fda61dbf3ddaad1b386d9d326… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Filter library dataset by user Commit: 5016a2d5251f42c87c22f1ad9d2bf164436f9ffd https://github.com/galaxyproject/galaxy/commit/5016a2d5251f42c87c22f1ad9d2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/visualization.py Log Message: ----------- Merge pull request #4836 from guerler/filter_visualization_grid [17.09] Add filter to visualization dataset queries Compare: https://github.com/galaxyproject/galaxy/compare/30b9e5e4afa2...5016a2d5251f

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[galaxyproject/galaxy] 1f6df5: Fix the spinner for the GIE container readiness ch...
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 1f6df5580bc27d89a93755502f792c711d07b4b5 https://github.com/galaxyproject/galaxy/commit/1f6df5580bc27d89a93755502f79… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.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: ----------- Fix the spinner for the GIE container readiness check. Commit: 30b9e5e4afa2c646a36213fa10d31fd1bc848c3e https://github.com/galaxyproject/galaxy/commit/30b9e5e4afa2c646a36213fa10d3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M client/galaxy/scripts/galaxy.interactive_environments.js M config/plugins/interactive_environments/jupyter/static/js/jupyter.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: ----------- Merge pull request #4835 from natefoo/gie-spinner-fix [17.09] Fix the spinner for the GIE container readiness check Compare: https://github.com/galaxyproject/galaxy/compare/9475e9aac106...30b9e5e4afa2

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[galaxyproject/infrastructure-playbook] a3a4bd: Stop emailing me every hour for biostar backups un...
by GitHub 20 Oct '17

20 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a3a4bd71a25c220ad48b214eb447d1a6b7a73128 https://github.com/galaxyproject/infrastructure-playbook/commit/a3a4bd71a25… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-20 (Fri, 20 Oct 2017) Changed paths: M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml Log Message: ----------- Stop emailing me every hour for biostar backups unless there's a problem

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[galaxyproject/usegalaxy-playbook] 98c3e5: Updated FLASh to 1.2.11.2
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 98c3e52eeacd6bd90ef78474909b527320d3d93b https://github.com/galaxyproject/usegalaxy-playbook/commit/98c3e52eeacd6bd9… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) 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: ----------- Updated FLASh to 1.2.11.2

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[galaxyproject/galaxy] 3b03b5: Fix for single select list initial value when mult...
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 3b03b5b6cca75fb93c114d93c97e29b8157869b8 https://github.com/galaxyproject/galaxy/commit/3b03b5b6cca75fb93c114d93c97e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix for single select list initial value when multiple options are selected by default. Commit: 9475e9aac1068538131bce8c047f89c3c4546bb8 https://github.com/galaxyproject/galaxy/commit/9475e9aac1068538131bce8c047f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #4834 from blankenberg/multiple-initial-single-select-param [17.09] Fix for single select list initial value when multiple options are selected by default. Compare: https://github.com/galaxyproject/galaxy/compare/acc59e4d5db4...9475e9aac106

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[galaxyproject/usegalaxy-playbook] d7a311: Real path corrections
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d7a311065b137937559f133c2c6a7750fe1137a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/d7a311065b137937… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M env/test/files/galaxy/config/object_store_conf.xml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Real path corrections

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[galaxyproject/usegalaxy-playbook] ee6baa: Update Test and fix old static path in Test nginx ...
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ee6baaa36a0b12ab6ec144e976ac2878ddad7b46 https://github.com/galaxyproject/usegalaxy-playbook/commit/ee6baaa36a0b12ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Update Test and fix old static path in Test nginx config.

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[galaxyproject/galaxy] 6d8948: Additional hardening for older releases
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Additional hardening for older releases Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases Commit: 34344a7563a3859c5171c65c3544ab8f7773fe2b https://github.com/galaxyproject/galaxy/commit/34344a7563a3859c5171c65c3544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into release_16.10 Commit: ae140949a8696a3b12aee83a9176e8091787a85d https://github.com/galaxyproject/galaxy/commit/ae140949a8696a3b12aee83a9176… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.10' into release_17.01 Commit: f0e9767912f91932d3541a3e824ebe026648cbf6 https://github.com/galaxyproject/galaxy/commit/f0e9767912f91932d3541a3e824e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Commit: acc59e4d5db43ae9f3430529605988a9743a8a6d https://github.com/galaxyproject/galaxy/commit/acc59e4d5db43ae9f34305296059… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' into release_17.09 Commit: 0447ec7ea0bb594c4d6d1df32b1013347b062408 https://github.com/galaxyproject/galaxy/commit/0447ec7ea0bb594c4d6d1df32b10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/be0541db9771...0447ec7ea0bb

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[galaxyproject/galaxy] 6d8948: Additional hardening for older releases
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Additional hardening for older releases Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases Commit: 34344a7563a3859c5171c65c3544ab8f7773fe2b https://github.com/galaxyproject/galaxy/commit/34344a7563a3859c5171c65c3544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into release_16.10 Commit: ae140949a8696a3b12aee83a9176e8091787a85d https://github.com/galaxyproject/galaxy/commit/ae140949a8696a3b12aee83a9176… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.10' into release_17.01 Commit: f0e9767912f91932d3541a3e824ebe026648cbf6 https://github.com/galaxyproject/galaxy/commit/f0e9767912f91932d3541a3e824e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Commit: acc59e4d5db43ae9f3430529605988a9743a8a6d https://github.com/galaxyproject/galaxy/commit/acc59e4d5db43ae9f34305296059… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.05' into release_17.09 Compare: https://github.com/galaxyproject/galaxy/compare/07e58a1cdf18...acc59e4d5db4

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[galaxyproject/galaxy] 6d8948: Additional hardening for older releases
by GitHub 19 Oct '17

19 Oct '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 6d8948217b0a106304ec4fe0f35bc9c4e73d9310 https://github.com/galaxyproject/galaxy/commit/6d8948217b0a106304ec4fe0f35b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-18 (Wed, 18 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Additional hardening for older releases Commit: 8e199a33cf2564f72cfb9e12ca71e48c873c6d5a https://github.com/galaxyproject/galaxy/commit/8e199a33cf2564f72cfb9e12ca71… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge pull request #4812 from natefoo/hardening-extras-16.07 [16.07] Additional hardening for older releases Commit: 34344a7563a3859c5171c65c3544ab8f7773fe2b https://github.com/galaxyproject/galaxy/commit/34344a7563a3859c5171c65c3544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.07' into release_16.10 Commit: ae140949a8696a3b12aee83a9176e8091787a85d https://github.com/galaxyproject/galaxy/commit/ae140949a8696a3b12aee83a9176… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_16.10' into release_17.01 Commit: f0e9767912f91932d3541a3e824ebe026648cbf6 https://github.com/galaxyproject/galaxy/commit/f0e9767912f91932d3541a3e824e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-19 (Thu, 19 Oct 2017) Changed paths: M lib/galaxy/datatypes/dataproviders/external.py M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py Log Message: ----------- Merge remote-tracking branch 'origin/release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/ef203a69e95f...f0e9767912f9

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