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

[galaxyproject/galaxy] a5d794: Add docs about running jobs in containers
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5d794dc4d1ee48539aa36c82ec56ac40760e0fa https://github.com/galaxyproject/galaxy/commit/a5d794dc4d1ee48539aa36c82ec5… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Add docs about running jobs in containers Explain how jobs can be run in containers (something currently documented in the `job_conf.xml.sample_advanced` file) Commit: 973c73ce722ae588d8aca9d5f71c6f6e938f10e4 https://github.com/galaxyproject/galaxy/commit/973c73ce722ae588d8aca9d5f71c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #6820 from pvanheus/patch-8 Add docs about running jobs in containers Compare: https://github.com/galaxyproject/galaxy/compare/13d92c007001...973c73ce722a **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 5b8ae3: Update to latest galaxy-lib.
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b8ae3e7314dbd96a13e8b32447fff6bdb358ae0 https://github.com/galaxyproject/galaxy/commit/5b8ae3e7314dbd96a13e8b32447f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Update to latest galaxy-lib. Commit: 13d92c007001b11a052f21b103c717a430861f66 https://github.com/galaxyproject/galaxy/commit/13d92c007001b11a052f21b103c7… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/lint.py M lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Merge pull request #6709 from jmchilton/galaxy-lib-update-20180913 Update to latest galaxy-lib. Compare: https://github.com/galaxyproject/galaxy/compare/997301cfe4c6...13d92c007001 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 4908b9: Fix types on "reserve_memory" / "reserve_cpu"
by GitHub 05 Oct '18

05 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4908b98daaf45aa886a3b0a7badcf90acb949c19 https://github.com/galaxyproject/galaxy/commit/4908b98daaf45aa886a3b0a7badc… Author: pvanheus <pvh(a)sanbi.ac.za> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M config/containers_conf.yml.sample Log Message: ----------- Fix types on "reserve_memory" / "reserve_cpu" resverve changed to reserve Commit: 997301cfe4c6ab1ec9596330c8267c73d465a3fc https://github.com/galaxyproject/galaxy/commit/997301cfe4c6ab1ec9596330c826… Author: Helena Rasche <erasche(a)users.noreply.github.com> Date: 2018-10-05 (Fri, 05 Oct 2018) Changed paths: M config/containers_conf.yml.sample Log Message: ----------- Merge pull request #6817 from pvanheus/patch-6 Fix typos on "reserve_memory" / "reserve_cpu" Compare: https://github.com/galaxyproject/galaxy/compare/18f351ae31ae...997301cfe4c6 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] b4e69c: Set a slurm reboot program so `scontrol reboot` wo...
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b4e69cd3abb082a412404d48111093d07fdc1513 https://github.com/galaxyproject/infrastructure-playbook/commit/b4e69cd3abb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Set a slurm reboot program so `scontrol reboot` works **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 4fcfff: Remove duplicate athena key
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 4fcfff08ea457d3fc91f8e99628bce66feea5b71 https://github.com/galaxyproject/infrastructure-playbook/commit/4fcfff08ea4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/common/group_vars/sslservers/vault.yml Log Message: ----------- Remove duplicate athena key Commit: 6bf8ecf5223028bb96092dd2018896b8b147dab4 https://github.com/galaxyproject/infrastructure-playbook/commit/6bf8ecf5223… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: A roles/dj-wasabi.telegraf/.github/ISSUE_TEMPLATE/bug_report.md A roles/dj-wasabi.telegraf/.github/ISSUE_TEMPLATE/feature_request.md M roles/dj-wasabi.telegraf/.travis.yml M roles/dj-wasabi.telegraf/CHANGELOG.md A roles/dj-wasabi.telegraf/CODE_OF_CONDUCT.md A roles/dj-wasabi.telegraf/CONTRIBUTING.md A roles/dj-wasabi.telegraf/LICENSE A roles/dj-wasabi.telegraf/PULL_REQUEST_TEMPLATE.md M roles/dj-wasabi.telegraf/README.md M roles/dj-wasabi.telegraf/defaults/main.yml M roles/dj-wasabi.telegraf/meta/.galaxy_install_info M roles/dj-wasabi.telegraf/meta/main.yml M roles/dj-wasabi.telegraf/molecule/default/create.yml M roles/dj-wasabi.telegraf/molecule/default/molecule.yml M roles/dj-wasabi.telegraf/molecule/default/playbook.yml M roles/dj-wasabi.telegraf/molecule/default/yaml-lint.yml A roles/dj-wasabi.telegraf/requirements.txt M roles/dj-wasabi.telegraf/tasks/Debian.yml M roles/dj-wasabi.telegraf/tasks/RedHat.yml A roles/dj-wasabi.telegraf/tasks/configure.yml M roles/dj-wasabi.telegraf/tasks/main.yml M roles/dj-wasabi.telegraf/templates/etc-opt-telegraf-telegraf.conf.j2 M roles/dj-wasabi.telegraf/templates/telegraf-extra-plugin.conf.j2 M roles/dj-wasabi.telegraf/templates/telegraf.conf.j2 Log Message: ----------- Update dj-wasabi.telegraf Commit: d0d15fa672f7604a46f7190677b305dbc988c9e3 https://github.com/galaxyproject/infrastructure-playbook/commit/d0d15fa672f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: A env/tacc/group_vars/galaxydbservers.yml M env/tacc/group_vars/galaxyservers.yml A env/tacc/group_vars/maingalaxydbservers.yml A env/tacc/group_vars/testgalaxydbservers.yml M env/tacc/inventory A env/tacc/templates/stats/galaxy_db_slurp.sh.j2 M roles/stats/templates/galaxy_slurp.py.j2 Log Message: ----------- Use telegraf for collecting (some) of the SQL stats, thanks to a protip from @erasche Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/85852a755a… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] fdaf9a: Link up workflow PRs
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: fdaf9ac8641cfa5fa0aad706310aec2b31692ac1 https://github.com/galaxyproject/galaxy/commit/fdaf9ac8641cfa5fa0aad706310a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09_announce.rst Log Message: ----------- Link up workflow PRs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 6076bb: Grant telegraf db access
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6076bb07984e4a9a81c127f79af24d80f18cbbe8 https://github.com/galaxyproject/usegalaxy-playbook/commit/6076bb07984e4a9a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/main/group_vars/dbservers/vault.yml M env/test/group_vars/dbservers/vault.yml Log Message: ----------- Grant telegraf db access **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 386229: Re-add removed PRs (bad merge I think)
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 386229d1ce58522be4bece11b8f9473f5dce56b9 https://github.com/galaxyproject/galaxy/commit/386229d1ce58522be4bece11b8f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Re-add removed PRs (bad merge I think) **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] d82025: Update admin users
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d82025c0ac001a925b50c4ae1ac803fed088c988 https://github.com/galaxyproject/usegalaxy-playbook/commit/d82025c0ac001a92… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Update admin users **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] eacec0: Update....
by GitHub 04 Oct '18

04 Oct '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: eacec03d10c00503fdbb4da107254c06082507bb https://github.com/galaxyproject/galaxy/commit/eacec03d10c00503fdbb4da10725… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Update.... Commit: 4d165a567139abc3b4ad3baac422c9c0ebbaf554 https://github.com/galaxyproject/galaxy/commit/4d165a567139abc3b4ad3baac422… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-04 (Thu, 04 Oct 2018) Changed paths: M doc/source/releases/18.09.rst M doc/source/releases/18.09_announce.rst Log Message: ----------- Merge branch '18.09_release_notes' of github.com:jmchilton/galaxy into 18.09_release_notes Compare: https://github.com/galaxyproject/galaxy/compare/afffd9bdaa66...4d165a567139 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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