- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] ed2d7a: Stop attempting to load broken and unusable report...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ed2d7a112cefff46a01de39152153a6726f8d994 https://github.com/galaxyproject/usegalaxy-playbook/commit/ed2d7a112cefff46… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxywebservers.yml M env/test/files/nginx/tacc-protected/index.html M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/nginx/tacc_protected.j2 Log Message: ----------- Stop attempting to load broken and unusable reports, remove most references. Commit: 8fdf33572ac1880c6e8a996aba55be25380307c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/8fdf33572ac1880c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M README.md M env/common/backup.yml M env/common/config.yml A env/common/group_vars/pulsargalaxyservers.yml A env/common/host_vars/br005.bridges.psc.edu.yml A env/common/host_vars/jetstream-iu0.galaxyproject.org.yml A env/common/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/common/host_vars/login2.stampede2.tacc.utexas.edu.yml M env/common/templates/supervisor/galaxy_impersonate.j2 M env/common/templates/supervisor/galaxy_reports.j2 M env/common/update.yml M env/main/group_vars/all.yml M env/main/group_vars/galaxyservers/vars.yml A env/main/group_vars/pulsargalaxyservers.yml M env/main/group_vars/pulsarservers/vars.yml A env/main/host_vars/br005.bridges.psc.edu.yml R env/main/host_vars/br005.bridges.psc.edu.yml A env/main/host_vars/jetstream-iu0.galaxyproject.org.yml R env/main/host_vars/jetstream-iu0.galaxyproject.org.yml A env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml R env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/main/host_vars/login2.stampede2.tacc.utexas.edu.yml R env/main/host_vars/login2.stampede2.tacc.utexas.edu.yml A env/test/group_vars/pulsargalaxyservers.yml M env/test/group_vars/pulsarservers/vars.yml A env/test/host_vars/br005.bridges.psc.edu.yml R env/test/host_vars/br005.bridges.psc.edu.yml A env/test/host_vars/jetstream-iu0.galaxyproject.org.yml R env/test/host_vars/jetstream-iu0.galaxyproject.org.yml A env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml R env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml R env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml Log Message: ----------- Main: - Move Galaxy to /pylon5 and Pulsar persistence dir to /home on Bridges - Deduplicate host vars - Get rid of instance_root and shared_root Commit: ca624a917495743923e16f08fd3bf17303ecf541 https://github.com/galaxyproject/usegalaxy-playbook/commit/ca624a9174957439… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/group_vars/pulsarservers/vars.yml Log Message: ----------- Set pulsar_port for Main pulsar on Jetstream Commit: ad1c1c7c3d759d0a6739e162a76097e77bff58df https://github.com/galaxyproject/usegalaxy-playbook/commit/ad1c1c7c3d759d0a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Main: update job_conf.xml for Bridges dir move Commit: 9c0270c4ddd43132dd0a024f881f99c4668393a9 https://github.com/galaxyproject/usegalaxy-playbook/commit/9c0270c4ddd43132… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Remove erroneous space that caused a YAML parsing error Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/97b3bb137b92...… **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] 97b3bb: Upgrade dexseq to 1.24
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 97b3bb137b92eb02fa97ebd46fbf1eb39893371b https://github.com/galaxyproject/usegalaxy-playbook/commit/97b3bb137b92eb02… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Upgrade dexseq to 1.24 **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] 34bc18: Add PB and EB to util.size_to_bytes, reorder match...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 34bc18025bfd63a916ff748fdfce98a139c1c2dd https://github.com/galaxyproject/galaxy/commit/34bc18025bfd63a916ff748fdfce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Add PB and EB to util.size_to_bytes, reorder match check so that the sizes more likely to be encountered are first. Commit: 3cd71b4864d2148e7bcdd18b7e12964ad409254a https://github.com/galaxyproject/galaxy/commit/3cd71b4864d2148e7bcdd18b7e12… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #6786 from natefoo/more-size-to-bytes Add PB and EB to util.size_to_bytes Compare: https://github.com/galaxyproject/galaxy/compare/5a9cdfe82694...3cd71b4864d2 **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] 270ee3: Add .yml extension to stampede2 host file
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 270ee3ee36a49da066dfd3f8c00edd99d908e802 https://github.com/galaxyproject/usegalaxy-playbook/commit/270ee3ee36a49da0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: R env/test/host_vars/login2.stampede2.tacc.utexas.edu A env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml Log Message: ----------- Add .yml extension to stampede2 host file Commit: a236263404a0e65505b29b7ed8109aa1fd2aad97 https://github.com/galaxyproject/usegalaxy-playbook/commit/a236263404a0e655… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/common/templates/supervisor/galaxy_datamanager.j2 M env/test/group_vars/all.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/pulsarservers/vars.yml M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/login2.stampede2.tacc.utexas.edu.yml Log Message: ----------- Test: - Stop using the confusing/limiting `shared_root` and `instance_root`. - Move Pular's state directory on Bridges to /home and move the Galaxy clone to /pylon5. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/ede6eea39c12...… **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] ede6ee: Changelog update for DESeq2 deps
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ede6eea39c12c658f52335bac9acc8071bf93e39 https://github.com/galaxyproject/usegalaxy-playbook/commit/ede6eea39c12c658… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M CHANGELOG.md Log Message: ----------- Changelog update for DESeq2 deps **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] e9e2b6: Minor reminders that would have been nice (for me, ...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9e2b6d9e22a141d6af1e47c2b77c0544f00b1ea https://github.com/galaxyproject/galaxy/commit/e9e2b6d9e22a141d6af1e47c2b77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Minor reminders that would have been nice (for me, at least) to have on the release scaffold. Commit: 5a9cdfe82694a5bb6be0eedce6502229779dd283 https://github.com/galaxyproject/galaxy/commit/5a9cdfe82694a5bb6be0eedce650… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #6778 from dannon/minor_rn_reminders Release issue scaffold tweaks Compare: https://github.com/galaxyproject/galaxy/compare/872b6f57ed7c...5a9cdfe82694 **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] becb92: Strip all control characters from rules
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: becb922dc1e8c2d48e03a2badcb940ab1661e247 https://github.com/galaxyproject/galaxy/commit/becb922dc1e8c2d48e03a2badcb9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Strip all control characters from rules Similar to 366701cfb23d8de31eac3c4312c6accca2e74ef1, which is valid on its own, but here we just apply it to all rules. Commit: c5a325d01535d9b46e28165c531a119d5f51b2d6 https://github.com/galaxyproject/galaxy/commit/c5a325d01535d9b46e28165c531a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/util/rules_dsl.py A test/unit/test_utils.py Log Message: ----------- Merge pull request #6785 from mvdbeek/escape_all_rules [18.09] Strip all control characters from rules Compare: https://github.com/galaxyproject/galaxy/compare/f54cba043354...c5a325d01535 **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] bf0370: Fix __encode_invocation signature and passthrough ...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: bf0370c1929def91bc69e1ab252dc0e8bfc2a387 https://github.com/galaxyproject/galaxy/commit/bf0370c1929def91bc69e1ab252d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix __encode_invocation signature and passthrough to manager that I busted in merging 18.05 forward Commit: da3b6a1566dc0bb2665b2781cdb3c76551d68613 https://github.com/galaxyproject/galaxy/commit/da3b6a1566dc0bb2665b2781cdb3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- encode_invocation defers to manager and doesn't require trans passing anymore Commit: f54cba043354aa8fac339052462f7302613ca24a https://github.com/galaxyproject/galaxy/commit/f54cba043354aa8fac339052462f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #6782 from dannon/fix-bad-workflow-invocation-merge [18.09] Fix __encode_invocation signature Compare: https://github.com/galaxyproject/galaxy/compare/b44379c3d9da...f54cba043354 **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] 3a5012: Test: Move Galaxy from /home to /pylon5 on Bridges...
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3a5012154ba4a3c759bb0b2da1dfcd96b59a7c5f https://github.com/galaxyproject/usegalaxy-playbook/commit/3a5012154ba4a3c7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Test: Move Galaxy from /home to /pylon5 on Bridges now that there is no quota on /pylon5 (and there is one on /home) **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] 0743c7: All extracted datasets should be visible
by GitHub 27 Sep '18

27 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 0743c7ba04fa6e61e2c48386a49a61f41d1eb493 https://github.com/galaxyproject/galaxy/commit/0743c7ba04fa6e61e2c48386a49a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- All extracted datasets should be visible Commit: b44379c3d9da4b7916b3c5a4fdf5eff39ee2267d https://github.com/galaxyproject/galaxy/commit/b44379c3d9da4b7916b3c5a4fdf5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #6780 from mvdbeek/visible_extracted_datasets [18.09] All extracted datasets should be visible Compare: https://github.com/galaxyproject/galaxy/compare/04d2d2ef4672...b44379c3d9da **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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