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

[galaxyproject/infrastructure-playbook] 132787: Update common roles
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 13278787f1b6a79a3cbd71bf89f5ae5997c60119 https://github.com/galaxyproject/infrastructure-playbook/commit/13278787f1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M common_roles Log Message: ----------- Update common roles Commit: 7da3234b2472fef8dc725870351728c180ff3d5f https://github.com/galaxyproject/infrastructure-playbook/commit/7da3234b247… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/galaxy/group_vars/jenkinsservers/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/jsiu/group_vars/controllers.yml M env/jstacc/group_vars/controllers.yml M env/tacc/group_vars/galaxyservers.yml M env/tacc/group_vars/slurmservers.yml M env/tacc/group_vars/statsservers/vars.yml Log Message: ----------- Update for crontabs role changes and disable mailoom for now Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/3f7c1e49dc…

1 0

[galaxyproject/usegalaxy-playbook] 871b55: update TTS
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 871b55824ccb22fb26ff01afb95b06adc4497fc2 https://github.com/galaxyproject/usegalaxy-playbook/commit/871b55824ccb22fb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS

1 0

[galaxyproject/galaxy] 3aa01b: initial pass fixing toolshed nav structure -- need...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3aa01b060477fe3fe0f59c73ca3ee75605e08182 https://github.com/galaxyproject/galaxy/commit/3aa01b060477fe3fe0f59c73ca3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- initial pass fixing toolshed nav structure -- need to follow up on dependencies Commit: 4d66d8025107bbeba5cf15ac5f177d600d7bf2d1 https://github.com/galaxyproject/galaxy/commit/4d66d8025107bbeba5cf15ac5f17… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/yarn.lock M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Fixes to toolshed/menu for BS4 Commit: cbaff1dca2e34cd869227844a04a761332a7eb27 https://github.com/galaxyproject/galaxy/commit/cbaff1dca2e34cd869227844a04a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Correct uWSGI UNIX domain socket syntax. Commit: 352ba5f634ff5469039afa4cb6ec5b6fecabe6c6 https://github.com/galaxyproject/galaxy/commit/352ba5f634ff5469039afa4cb6ec… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js Log Message: ----------- show tooltip only on hover for upload button Commit: 5265e93be9fc2cf8c65400d8c1853169377868a9 https://github.com/galaxyproject/galaxy/commit/5265e93be9fc2cf8c65400d8c185… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js Log Message: ----------- move some tooltips to the top so they don't interfere with other actions when shown Commit: 20e9e0a018967e413380728275b843615ba0c6f4 https://github.com/galaxyproject/galaxy/commit/20e9e0a018967e413380728275b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Format 'logged in as' correctly for the toolshed Commit: 103cb51ec368438642504c3f98b76c363db478bb https://github.com/galaxyproject/galaxy/commit/103cb51ec368438642504c3f98b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #6003 from natefoo/uwsgi-socket-docs [18.01] Correct uWSGI UNIX domain socket syntax in docs Commit: bf0543743ff832375e1b7128bdaa4fc5b0714038 https://github.com/galaxyproject/galaxy/commit/bf0543743ff832375e1b7128bdaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/upload/upload-button.js Log Message: ----------- Merge remote-tracking branch 'martenson/tooltip-ux' into release_18.05 Commit: 3a45c1617a0f2b24c6cea344a30aab51c36947ce https://github.com/galaxyproject/galaxy/commit/3a45c1617a0f2b24c6cea344a30a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/yarn.lock Log Message: ----------- Client build/format on merge to 18.05 Commit: 4a7bc238a6ed80d3e2791bd567e5f2c0e8edb3a8 https://github.com/galaxyproject/galaxy/commit/4a7bc238a6ed80d3e2791bd567e5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #5979 from dannon/fix_toolshed_nav Fix toolshed nav for BS4 Commit: 916078beb0b5936644e666dc91b6c99e8f6aab35 https://github.com/galaxyproject/galaxy/commit/916078beb0b5936644e666dc91b6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: acc9889815460b7f7ac4652e226e9f9209f8fc9d https://github.com/galaxyproject/galaxy/commit/acc9889815460b7f7ac4652e226e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/yarn.lock M doc/source/admin/scaling.md M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6a8c4dc7e287...acc988981546

1 0

[galaxyproject/galaxy] cbaff1: Correct uWSGI UNIX domain socket syntax.
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: cbaff1dca2e34cd869227844a04a761332a7eb27 https://github.com/galaxyproject/galaxy/commit/cbaff1dca2e34cd869227844a04a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Correct uWSGI UNIX domain socket syntax. Commit: 103cb51ec368438642504c3f98b76c363db478bb https://github.com/galaxyproject/galaxy/commit/103cb51ec368438642504c3f98b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #6003 from natefoo/uwsgi-socket-docs [18.01] Correct uWSGI UNIX domain socket syntax in docs Commit: 916078beb0b5936644e666dc91b6c99e8f6aab35 https://github.com/galaxyproject/galaxy/commit/916078beb0b5936644e666dc91b6… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/4a7bc238a6ed...916078beb0b5

1 0

[galaxyproject/galaxy] 3aa01b: initial pass fixing toolshed nav structure -- need...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 3aa01b060477fe3fe0f59c73ca3ee75605e08182 https://github.com/galaxyproject/galaxy/commit/3aa01b060477fe3fe0f59c73ca3e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- initial pass fixing toolshed nav structure -- need to follow up on dependencies Commit: 4d66d8025107bbeba5cf15ac5f177d600d7bf2d1 https://github.com/galaxyproject/galaxy/commit/4d66d8025107bbeba5cf15ac5f17… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M client/yarn.lock M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Fixes to toolshed/menu for BS4 Commit: 20e9e0a018967e413380728275b843615ba0c6f4 https://github.com/galaxyproject/galaxy/commit/20e9e0a018967e413380728275b8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Format 'logged in as' correctly for the toolshed Commit: 4a7bc238a6ed80d3e2791bd567e5f2c0e8edb3a8 https://github.com/galaxyproject/galaxy/commit/4a7bc238a6ed80d3e2791bd567e5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/toolshed/groups/group-list-view.js M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #5979 from dannon/fix_toolshed_nav Fix toolshed nav for BS4 Compare: https://github.com/galaxyproject/galaxy/compare/3a45c1617a0f...4a7bc238a6ed

1 0

[galaxyproject/galaxy] 352ba5: show tooltip only on hover for upload button
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 352ba5f634ff5469039afa4cb6ec5b6fecabe6c6 https://github.com/galaxyproject/galaxy/commit/352ba5f634ff5469039afa4cb6ec… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/upload-button.js Log Message: ----------- show tooltip only on hover for upload button Commit: 5265e93be9fc2cf8c65400d8c1853169377868a9 https://github.com/galaxyproject/galaxy/commit/5265e93be9fc2cf8c65400d8c185… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js Log Message: ----------- move some tooltips to the top so they don't interfere with other actions when shown Commit: bf0543743ff832375e1b7128bdaa4fc5b0714038 https://github.com/galaxyproject/galaxy/commit/bf0543743ff832375e1b7128bdaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/upload/upload-button.js Log Message: ----------- Merge remote-tracking branch 'martenson/tooltip-ux' into release_18.05 Commit: 3a45c1617a0f2b24c6cea344a30aab51c36947ce https://github.com/galaxyproject/galaxy/commit/3a45c1617a0f2b24c6cea344a30a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/yarn.lock Log Message: ----------- Client build/format on merge to 18.05 Compare: https://github.com/galaxyproject/galaxy/compare/bd63c04c2e19...3a45c1617a0f

1 0

[galaxyproject/galaxy] cbaff1: Correct uWSGI UNIX domain socket syntax.
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cbaff1dca2e34cd869227844a04a761332a7eb27 https://github.com/galaxyproject/galaxy/commit/cbaff1dca2e34cd869227844a04a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Correct uWSGI UNIX domain socket syntax. Commit: 103cb51ec368438642504c3f98b76c363db478bb https://github.com/galaxyproject/galaxy/commit/103cb51ec368438642504c3f98b7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #6003 from natefoo/uwsgi-socket-docs [18.01] Correct uWSGI UNIX domain socket syntax in docs Compare: https://github.com/galaxyproject/galaxy/compare/26ab5388ba31...103cb51ec368

1 0

[galaxyproject/infrastructure-playbook] 3f7c1e: Ensure yum will only keep at most 2 kernels around...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3f7c1e49dc527726bdc551f629a79adc6fcf0b2a https://github.com/galaxyproject/infrastructure-playbook/commit/3f7c1e49dc5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/tacc/playbook.yml Log Message: ----------- Ensure yum will only keep at most 2 kernels around on TACC hosts, to avoid filling up /boot

1 0

[galaxyproject/usegalaxy-playbook] 1e5583: fix the resizing overlap
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e5583483fa5b3f87736c4f924dfdb5c573a0b44 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e5583483fa5b3f8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- fix the resizing overlap reported in https://github.com/galaxyproject/galaxy/issues/6002

1 0

[galaxyproject/galaxy] 50f9ca: Don't attempt to determine ports at GIE container ...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50f9ca82ba158736e7ed735e3d949a65127a5111 https://github.com/galaxyproject/galaxy/commit/50f9ca82ba158736e7ed735e3d94… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Don't attempt to determine ports at GIE container launch time if they fail to be determined on the first attempt. They'll be determined by the readiness check instead. Commit: a7a4e12e79a91a2a17fa86d65077233f8cfcb35c https://github.com/galaxyproject/galaxy/commit/a7a4e12e79a91a2a17fa86d65077… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix collection element count getting lost during collection copies. Commit: 3c7bffb8352fb419d9ca2ff2c5d1bbdf26d8a7b6 https://github.com/galaxyproject/galaxy/commit/3c7bffb8352fb419d9ca2ff2c5d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix ftp imports in rule builder. Commit: 8470815163336d54078b713452ae9dcd58dfe53f https://github.com/galaxyproject/galaxy/commit/8470815163336d54078b713452ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Fix add row number rule. Commit: a29770ca554b5aaf8ea6533ee413fed77042a0ea https://github.com/galaxyproject/galaxy/commit/a29770ca554b5aaf8ea6533ee413… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Pin the version of node we use in CI, etc.... Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well). Commit: c7b426089aa7ec0e0ba874e03ed9dad60a9d1909 https://github.com/galaxyproject/galaxy/commit/c7b426089aa7ec0e0ba874e03ed9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #6000 from jmchilton/fix_build_maybe [18.01] Backport #5972 Commit: e3331817283bdffa4a6fbf65627f44a1faf61239 https://github.com/galaxyproject/galaxy/commit/e3331817283bdffa4a6fbf65627f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge pull request #5991 from jmchilton/rule_fixes_2 [18.05] Small Rule Builder Fixes Commit: 9da13d2d3d3a444e9cd45880496c883b30b475b0 https://github.com/galaxyproject/galaxy/commit/9da13d2d3d3a444e9cd45880496c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #5990 from jmchilton/collection_count_fix [18.01] Fix collection element count getting lost during collection copies. Commit: 26ab5388ba31de646d365fbc8528a86b7dc7949a https://github.com/galaxyproject/galaxy/commit/26ab5388ba31de646d365fbc8528… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge pull request #5930 from natefoo/gie-late-ports [18.01] Only try to determine GIE container ports once at launch, then hand off to readiness check Commit: bd63c04c2e1988e838a033830f60e1ad6c2d9bf7 https://github.com/galaxyproject/galaxy/commit/bd63c04c2e1988e838a033830f60… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/containers/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.01' into release_18.05 Commit: 6a8c4dc7e287c83c335879e02caa61493d2aa967 https://github.com/galaxyproject/galaxy/commit/6a8c4dc7e287c83c335879e02caa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M lib/galaxy/containers/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/visualization/plugins/interactive_environments.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py Log Message: ----------- Merge remote-tracking branch 'origin/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/39dd9ac76c4d...6a8c4dc7e287

1 0