- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 968bc9: Correct slurm_user format (why didn't this cause f...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 968bc99aa90fdd56959e7af6ea73e6e86e083893 https://github.com/galaxyproject/infrastructure-playbook/commit/968bc99aa90… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/tacc/group_vars/slurmclients/vars.yml Log Message: ----------- Correct slurm_user format (why didn't this cause failures?) Commit: be0fb386736f8999433559cc0d2403ca59f98529 https://github.com/galaxyproject/infrastructure-playbook/commit/be0fb386736… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M env/tacc/group_vars/all.yml Log Message: ----------- Add mount definition for switching NFS servers as needed Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/654ae08ccf…

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[galaxyproject/galaxy] 5522c7: Add `index` to OIDC controller to list authnzs ass...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5522c78d9d1ebcb490285528a8587ff7157a6d6d https://github.com/galaxyproject/galaxy/commit/5522c78d9d1ebcb490285528a858… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Add `index` to OIDC controller to list authnzs associated with a user. Commit: 68dad22d1e15a30d8ee49f2f8002cdd7d7dfc723 https://github.com/galaxyproject/galaxy/commit/68dad22d1e15a30d8ee49f2f8002… Author: vjalili <jalili.vahid(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Add router to authnz index. Commit: 881dc3601823da61c3a883f17907132f07afd0bd https://github.com/galaxyproject/galaxy/commit/881dc3601823da61c3a883f17907… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/authnz.py Log Message: ----------- Merge pull request #5908 from VJalili/oidc_index OIDC controller index Compare: https://github.com/galaxyproject/galaxy/compare/b71a163a8ce8...881dc3601823

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[galaxyproject/galaxy] 100904: Add OIDC and OAuth2.0 config to authentication doc...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 10090476267c1a2cec8103c4d3844057e682c730 https://github.com/galaxyproject/galaxy/commit/10090476267c1a2cec8103c4d384… Author: Vahid <VJalili(a)users.noreply.github.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Add OIDC and OAuth2.0 config to authentication docs Commit: b71a163a8ce84403cec829e12265573e44d4f668 https://github.com/galaxyproject/galaxy/commit/b71a163a8ce84403cec829e12265… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M doc/source/admin/authentication.md Log Message: ----------- Merge pull request #5906 from VJalili/patch-6 Add OIDC and OAuth2.0 config to authentication docs Compare: https://github.com/galaxyproject/galaxy/compare/60b5a9a52ab8...b71a163a8ce8

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[galaxyproject/galaxy] b24a1b: Small fix for workflow editor Selenium testing.
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b24a1b723dd0d378b5f5c181f74f3340409839d8 https://github.com/galaxyproject/galaxy/commit/b24a1b723dd0d378b5f5c181f74f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/test_workflow_editor.py Log Message: ----------- Small fix for workflow editor Selenium testing. Commit: 54721122e7439eeea2d2c6840ed668f827eed577 https://github.com/galaxyproject/galaxy/commit/54721122e7439eeea2d2c6840ed6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Small fixes, enhancements for workflow run Selenium tests. Commit: 8f529d177ada3ef179a982d05dd4f04ba82e8abe https://github.com/galaxyproject/galaxy/commit/8f529d177ada3ef179a982d05dd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M test/api/test_workflows.py M test/base/workflow_fixtures.py Log Message: ----------- Improve a few workflow run API test cases. Use the more abstract test_data specification that will translate to GUI testing. Commit: aafd9de76ba61e2e3b2467188bb53e93c8b6fb2b https://github.com/galaxyproject/galaxy/commit/aafd9de76ba61e2e3b2467188bb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-13 (Fri, 13 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Add more complicated workflow run test case. Re-use test_data specification used by many of the API workflow tests and a workflow used by another test. Add abstractions and DOM element for mapping labeled test data to tool form inputs. Commit: 60b5a9a52ab853bf9ff3adf09bbcc6ae0c4d7992 https://github.com/galaxyproject/galaxy/commit/60b5a9a52ab853bf9ff3adf09bbc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M test/api/test_workflows.py M test/base/populators.py M test/base/workflow_fixtures.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py Log Message: ----------- Merge pull request #5886 from jmchilton/selenium_workflow_run More, better workflow run Selenium tests. Compare: https://github.com/galaxyproject/galaxy/compare/3922065d8a29...60b5a9a52ab8

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[galaxyproject/infrastructure-playbook] 654ae0: Create slurm log directory and rotate logs
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 654ae08ccf30844b0f5b7332e32f20703d66c0ed https://github.com/galaxyproject/infrastructure-playbook/commit/654ae08ccf3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A roles/slurm/files/logrotate-slurm M roles/slurm/tasks/main.yml M roles/slurm/tasks/slurmd.yml Log Message: ----------- Create slurm log directory and rotate logs

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[galaxyproject/galaxy] 767a45: Fix proxy, add logo and example file to repo for h...
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 767a456544335b302a9c9b42fba30df34c61c296 https://github.com/galaxyproject/galaxy/commit/767a456544335b302a9c9b42fba3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A config/plugins/visualizations/hivtrace/static/logo.png M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Fix proxy, add logo and example file to repo for hivtrace Delete example file Commit: 3922065d8a294b609a2b2f9c2a89cbb0f192b9b4 https://github.com/galaxyproject/galaxy/commit/3922065d8a294b609a2b2f9c2a89… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: A config/plugins/visualizations/hivtrace/static/logo.png M config/plugins/visualizations/hivtrace/templates/index.mako Log Message: ----------- Merge pull request #5902 from guerler/add_logo_hivtrace Add proxy, logo and example file for hivtrace Compare: https://github.com/galaxyproject/galaxy/compare/19ed0e224235...3922065d8a29

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[galaxyproject/galaxy] cfa48d: Remove unused client route
by GitHub 18 Apr '18

18 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfa48d4aa6c1602a7bdef578ccbc31653a75ee26 https://github.com/galaxyproject/galaxy/commit/cfa48d4aa6c1602a7bdef578ccbc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Remove unused client route Commit: 19ed0e224235a5b10ce34d012d06075f07ea4a0c https://github.com/galaxyproject/galaxy/commit/19ed0e224235a5b10ce34d012d06… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Merge pull request #5907 from guerler/remove_unused_route Remove unused client route Compare: https://github.com/galaxyproject/galaxy/compare/5d82c1a09f9a...19ed0e224235

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[galaxyproject/infrastructure-playbook] aba8bf: Fix vars files for slurm on Jetstream
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: aba8bf0cd1b845e0ad3f7fb4d9f0818d238a4f3a https://github.com/galaxyproject/infrastructure-playbook/commit/aba8bf0cd1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/jscommon/group_vars/slurmclients/vars.yml R env/jsiu/group_vars/slurmclients.yml A env/jsiu/group_vars/slurmclients/common_vars.yml A env/jsiu/group_vars/slurmclients/common_vault.yml A env/jsiu/group_vars/slurmclients/vars.yml R env/jstacc/group_vars/slurmclients.yml A env/jstacc/group_vars/slurmclients/common_vars.yml A env/jstacc/group_vars/slurmclients/common_vault.yml A env/jstacc/group_vars/slurmclients/vars.yml Log Message: ----------- Fix vars files for slurm on Jetstream

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[galaxyproject/usegalaxy-playbook] bfbeca: update test
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bfbecad6a84fec79403ed876b16b3b99b1295944 https://github.com/galaxyproject/usegalaxy-playbook/commit/bfbecad6a84fec79… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-12 (Thu, 12 Apr 2018) Changed paths: M common_roles M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- update test Commit: 16bf5fb4e35961a1831d4ba3357ba9151605a955 https://github.com/galaxyproject/usegalaxy-playbook/commit/16bf5fb4e35961a1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- swap back to dev, remove message Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a6bd075e83b6...…

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[galaxyproject/infrastructure-playbook] b0158b: Fix errors with missing dict members
by GitHub 17 Apr '18

17 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b0158b830f1fb9980ce1f35db32f503a46bcd338 https://github.com/galaxyproject/infrastructure-playbook/commit/b0158b830f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml M roles/cvmfs/defaults/main.yml Log Message: ----------- Fix errors with missing dict members Commit: 502d8e6ef29fdc0dc17c4e08088553c5e9357139 https://github.com/galaxyproject/infrastructure-playbook/commit/502d8e6ef29… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-17 (Tue, 17 Apr 2018) Changed paths: M env/jscommon/templates/slurm/slurm.conf.j2 M env/tacc/templates/slurm/slurm.conf.j2 A roles/slurm/defaults/main.yml M roles/slurm/tasks/main.yml M roles/slurm/tasks/slurmctld.yml M roles/slurm/tasks/slurmd.yml M roles/slurm/tasks/slurmdbd.yml Log Message: ----------- Slurm upgrades Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/430f65ff7e…

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