- galaxy-commits - lists.galaxyproject.org

[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

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[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

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[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

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[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

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[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

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

27 Apr '18

Branch: refs/heads/release_18.05 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: 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/e3331817283b...bd63c04c2e19

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[galaxyproject/usegalaxy-playbook] fc7b2d: Add a banner to main about Slurm cgroup changes
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fc7b2dadd9d5e3e11335a884126e4680b7992ae6 https://github.com/galaxyproject/usegalaxy-playbook/commit/fc7b2dadd9d5e3e1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Add a banner to main about Slurm cgroup changes

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

27 Apr '18

Branch: refs/heads/release_18.01 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/9da13d2d3d3a...26ab5388ba31

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[galaxyproject/galaxy] a7a4e1: Fix collection element count getting lost during c...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy 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: 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. Compare: https://github.com/galaxyproject/galaxy/compare/c7b426089aa7...9da13d2d3d3a

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[galaxyproject/galaxy] 74939a: Update release process - do not require merge PRs ...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 74939a3f11a7b21d95e6da54cc26b53a0af854fc https://github.com/galaxyproject/galaxy/commit/74939a3f11a7b21d95e6da54cc26… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Update release process - do not require merge PRs to have milestones. Commit: 39dd9ac76c4de56dcc0066a08d0beba788a9bc93 https://github.com/galaxyproject/galaxy/commit/39dd9ac76c4de56dcc0066a08d0b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6004 from jmchilton/release_process_tweaks Update release process - do not require merge PRs to have milestones. Compare: https://github.com/galaxyproject/galaxy/compare/24b04bfef06d...39dd9ac76c4d

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[galaxyproject/galaxy] 3c7bff: Fix ftp imports in rule builder.
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/7ce49394c3a7...e3331817283b

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[galaxyproject/infrastructure-playbook] eb08fd: Enable cgroup config for Slurm
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: eb08fdb717525ed41333153921f16e98a17ff0d9 https://github.com/galaxyproject/infrastructure-playbook/commit/eb08fdb7175… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 M roles/slurm/tasks/slurmd.yml Log Message: ----------- Enable cgroup config for Slurm Commit: b775af709c252d7c6e0a6e541d846e5896b16340 https://github.com/galaxyproject/infrastructure-playbook/commit/b775af709c2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/tacc/group_vars/slurmservers.yml M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Decrease slurm daemon log level and stop emailing me spartbalance output Commit: d4afa568a7cb6f5ae86e1fb71bd6eda9afd9588e https://github.com/galaxyproject/infrastructure-playbook/commit/d4afa568a7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/tacc/files/slurm/spartbalance Log Message: ----------- Decrease minimum "normal" nodes allocated by spartbalance to 4 (matches slurm.conf) Commit: 5298b74ac861019f857cf90f0dc003a9eef13167 https://github.com/galaxyproject/infrastructure-playbook/commit/5298b74ac86… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- roundup57 has some bad memory, decrease its configured mem in slurm Commit: 4bd8d003474eb97efd686b0ef7b2d439be4fb97e https://github.com/galaxyproject/infrastructure-playbook/commit/4bd8d003474… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Add cgroup tools to nodes for cgroup metrics Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/73dc2d961d…

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[galaxyproject/galaxy] 482469: Optimize safe_walk to call realpath a lot less for...
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4824690ade9042c1c96de469a2c3218d2fc33c9a https://github.com/galaxyproject/galaxy/commit/4824690ade9042c1c96de469a2c3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Optimize safe_walk to call realpath a lot less for typical calls... Cuts the time required to load 100,000 FTP files into the rule builder in half on my macbook - could imagine the gains to be even bigger on a network file system? Commit: 24b04bfef06d0de9adbff82ce42e7b486fb0c8e9 https://github.com/galaxyproject/galaxy/commit/24b04bfef06d0de9adbff82ce42e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-27 (Fri, 27 Apr 2018) Changed paths: M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #5995 from jmchilton/ftp_optimize Optimize safe_walk to call realpath a lot less for typical calls... Compare: https://github.com/galaxyproject/galaxy/compare/7d9c085b03d4...24b04bfef06d

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[galaxyproject/galaxy] a29770: Pin the version of node we use in CI, etc....
by GitHub 27 Apr '18

27 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/a3e69636662c...c7b426089aa7

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[galaxyproject/galaxy] cd9db0: Provide ToolDataTableManager for backwards compati...
by GitHub 26 Apr '18

26 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cd9db0bffa68cec4891f38db77af578757d3b63d https://github.com/galaxyproject/galaxy/commit/cd9db0bffa68cec4891f38db77af… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Provide ToolDataTableManager for backwards compatibility Broken in 7df9dce63d635d66a0a9ce5045135ab49b7ef506 Commit: dbb08fe7620610812189049481740215c12f9eb6 https://github.com/galaxyproject/galaxy/commit/dbb08fe762061081218904948174… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5980 from martenson/version-18.05 [18.05] Update version to 18.05.rc1 Commit: 1b1962ea490cdf3f7ff97bfc0f570235ef8ad7fc https://github.com/galaxyproject/galaxy/commit/1b1962ea490cdf3f7ff97bfc0f57… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge pull request #5924 from mvdbeek/fix_data_managers [18.01] Provide ToolDataTableManager for backwards compatibility Commit: 7d81d2cfcba070558dbb1cb5e7b5be390e797ff3 https://github.com/galaxyproject/galaxy/commit/7d81d2cfcba070558dbb1cb5e7b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Fix 2 typos in the docs Commit: d5ec01d5da1dfde88090afec6df958dfa98af21c https://github.com/galaxyproject/galaxy/commit/d5ec01d5da1dfde88090afec6df9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5986 from nsoranzo/release_17.09_doc_fixes [17.09] Fix 2 typos in the docs Commit: a3e69636662cfeae0ebc1b66fcc03b0b7fe13be8 https://github.com/galaxyproject/galaxy/commit/a3e69636662cfeae0ebc1b66fcc0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 7ce49394c3a73fc64e23603ffcab8f39ff3159a0 https://github.com/galaxyproject/galaxy/commit/7ce49394c3a73fc64e23603ffcab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 7d9c085b03d477fa8322e140732d4d1c804d6a6a https://github.com/galaxyproject/galaxy/commit/7d9c085b03d477fa8322e140732d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/7580a28b3917...7d9c085b03d4

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[galaxyproject/galaxy] cd9db0: Provide ToolDataTableManager for backwards compati...
by GitHub 26 Apr '18

26 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: cd9db0bffa68cec4891f38db77af578757d3b63d https://github.com/galaxyproject/galaxy/commit/cd9db0bffa68cec4891f38db77af… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Provide ToolDataTableManager for backwards compatibility Broken in 7df9dce63d635d66a0a9ce5045135ab49b7ef506 Commit: 1b1962ea490cdf3f7ff97bfc0f570235ef8ad7fc https://github.com/galaxyproject/galaxy/commit/1b1962ea490cdf3f7ff97bfc0f57… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge pull request #5924 from mvdbeek/fix_data_managers [18.01] Provide ToolDataTableManager for backwards compatibility Commit: 7d81d2cfcba070558dbb1cb5e7b5be390e797ff3 https://github.com/galaxyproject/galaxy/commit/7d81d2cfcba070558dbb1cb5e7b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Fix 2 typos in the docs Commit: d5ec01d5da1dfde88090afec6df958dfa98af21c https://github.com/galaxyproject/galaxy/commit/d5ec01d5da1dfde88090afec6df9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5986 from nsoranzo/release_17.09_doc_fixes [17.09] Fix 2 typos in the docs Commit: a3e69636662cfeae0ebc1b66fcc03b0b7fe13be8 https://github.com/galaxyproject/galaxy/commit/a3e69636662cfeae0ebc1b66fcc0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Commit: 7ce49394c3a73fc64e23603ffcab8f39ff3159a0 https://github.com/galaxyproject/galaxy/commit/7ce49394c3a73fc64e23603ffcab… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/dbb08fe76206...7ce49394c3a7

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[galaxyproject/galaxy] 7d81d2: Fix 2 typos in the docs
by GitHub 26 Apr '18

26 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7d81d2cfcba070558dbb1cb5e7b5be390e797ff3 https://github.com/galaxyproject/galaxy/commit/7d81d2cfcba070558dbb1cb5e7b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Fix 2 typos in the docs Commit: d5ec01d5da1dfde88090afec6df958dfa98af21c https://github.com/galaxyproject/galaxy/commit/d5ec01d5da1dfde88090afec6df9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5986 from nsoranzo/release_17.09_doc_fixes [17.09] Fix 2 typos in the docs Commit: a3e69636662cfeae0ebc1b66fcc03b0b7fe13be8 https://github.com/galaxyproject/galaxy/commit/a3e69636662cfeae0ebc1b66fcc0… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Compare: https://github.com/galaxyproject/galaxy/compare/1b1962ea490c...a3e69636662c

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[galaxyproject/galaxy] 7d81d2: Fix 2 typos in the docs
by GitHub 26 Apr '18

26 Apr '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 7d81d2cfcba070558dbb1cb5e7b5be390e797ff3 https://github.com/galaxyproject/galaxy/commit/7d81d2cfcba070558dbb1cb5e7b5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Fix 2 typos in the docs Commit: d5ec01d5da1dfde88090afec6df958dfa98af21c https://github.com/galaxyproject/galaxy/commit/d5ec01d5da1dfde88090afec6df9… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M config/local_conda_mapping.yml.sample M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #5986 from nsoranzo/release_17.09_doc_fixes [17.09] Fix 2 typos in the docs Compare: https://github.com/galaxyproject/galaxy/compare/8e6cdd73aa4d...d5ec01d5da1d

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[galaxyproject/usegalaxy-playbook] fc764f: Test: collect cgroup metrics
by GitHub 26 Apr '18

26 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fc764f5d40d1b46e5fc45b67d365b3c90682c672 https://github.com/galaxyproject/usegalaxy-playbook/commit/fc764f5d40d1b46e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-26 (Thu, 26 Apr 2018) Changed paths: M env/test/files/galaxy/config/job_metrics_conf.xml Log Message: ----------- Test: collect cgroup metrics

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[galaxyproject/usegalaxy-playbook] 2da245: update Test
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2da245b487e90bf91dc67f284d895582b2e95ef7 https://github.com/galaxyproject/usegalaxy-playbook/commit/2da245b487e90bf9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update Test

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[galaxyproject/galaxy] cd9db0: Provide ToolDataTableManager for backwards compati...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cd9db0bffa68cec4891f38db77af578757d3b63d https://github.com/galaxyproject/galaxy/commit/cd9db0bffa68cec4891f38db77af… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Provide ToolDataTableManager for backwards compatibility Broken in 7df9dce63d635d66a0a9ce5045135ab49b7ef506 Commit: 1b1962ea490cdf3f7ff97bfc0f570235ef8ad7fc https://github.com/galaxyproject/galaxy/commit/1b1962ea490cdf3f7ff97bfc0f57… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge pull request #5924 from mvdbeek/fix_data_managers [18.01] Provide ToolDataTableManager for backwards compatibility Compare: https://github.com/galaxyproject/galaxy/compare/e68eaeecbf66...1b1962ea490c

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[galaxyproject/galaxy] 8d4666: Update version to 18.05.rc1
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 8d4666578d4dc2c0374ef105659d69931efa1f4e https://github.com/galaxyproject/galaxy/commit/8d4666578d4dc2c0374ef105659d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.rc1 Commit: dbb08fe7620610812189049481740215c12f9eb6 https://github.com/galaxyproject/galaxy/commit/dbb08fe762061081218904948174… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5980 from martenson/version-18.05 [18.05] Update version to 18.05.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/c41c84eec6e8...dbb08fe76206

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[galaxyproject/galaxy] 8d4666: Update version to 18.05.rc1
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d4666578d4dc2c0374ef105659d69931efa1f4e https://github.com/galaxyproject/galaxy/commit/8d4666578d4dc2c0374ef105659d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.rc1 Commit: 53e67733660a8061a31de1a2a867e46e35fa2465 https://github.com/galaxyproject/galaxy/commit/53e67733660a8061a31de1a2a867… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09.dev Commit: 8b51c30aa7c1e7ea711e22f81a4156ea1bcda769 https://github.com/galaxyproject/galaxy/commit/8b51c30aa7c1e7ea711e22f81a41… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Log Message: ----------- Merge branch 'version-18.05' into version-18.09.dev Commit: 7580a28b39175c221525abf74c0438a89b59f13f https://github.com/galaxyproject/galaxy/commit/7580a28b39175c221525abf74c04… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5982 from martenson/version-18.09.dev start Version 18.09.dev Compare: https://github.com/galaxyproject/galaxy/compare/c41c84eec6e8...7580a28b3917

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[galaxyproject/galaxy] e58034: Correct examples in dynamic job conf doc, remove h...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Commit: c41c84eec6e8cfc6291dd85ce58ba4b34b394bb1 https://github.com/galaxyproject/galaxy/commit/c41c84eec6e8cfc6291dd85ce58b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c1e5fb829016...c41c84eec6e8

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[galaxyproject/galaxy] e58034: Correct examples in dynamic job conf doc, remove h...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Commit: c41c84eec6e8cfc6291dd85ce58ba4b34b394bb1 https://github.com/galaxyproject/galaxy/commit/c41c84eec6e8cfc6291dd85ce58b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c1e5fb829016...c41c84eec6e8

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