galaxy-commits September 2018

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[galaxyproject/galaxy] c51178: Four more PRs
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: c51178578dcf67c8dbe16d3d8320f660e0c80027 https://github.com/galaxyproject/galaxy/commit/c51178578dcf67c8dbe16d3d8320… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Four more 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/galaxy] b0dff4: allow making all datasets within history public, w...
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b0dff4444085668cc3359b73d9d4d13b6da74cf6 https://github.com/galaxyproject/galaxy/commit/b0dff4444085668cc3359b73d9d4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- allow making all datasets within history public, when sharing this is a one-off operation so notable behavior is that if you create a new dataset in the shared history, it still won't be public when there are default permissions set on history Commit: e4399021520440a8f58e33dbae161f031f8da9eb https://github.com/galaxyproject/galaxy/commit/e4399021520440a8f58e33dbae16… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/web/base/controller.py Log Message: ----------- show warning to user if some of the items within were not published Commit: 29a3b6bbfbde469e59f6a896dc8a4f76a8d3ea3d https://github.com/galaxyproject/galaxy/commit/29a3b6bbfbde469e59f6a896dc8a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M client/galaxy/scripts/components/Sharing.vue M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py Log Message: ----------- Merge pull request #6793 from martenson/fix-sharing-by-link [18.09] allow making all datasets within history public, when sharing Compare: https://github.com/galaxyproject/galaxy/compare/5a98515df88b...29a3b6bbfbde **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] 53b062: Add bam upload test
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 53b062f804c6d495b187656c84597f953210a2b0 https://github.com/galaxyproject/galaxy/commit/53b062f804c6d495b187656c8459… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Add bam upload test `test_upload_bam_file` fails on release_18.09 but passes on 18.05. Commit: 57fe3a741a9c3ac9c09513e21d44984ba046322e https://github.com/galaxyproject/galaxy/commit/57fe3a741a9c3ac9c09513e21d44… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Fix metadata spontaneuosly reverting Similar to https://github.com/galaxyproject/galaxy/pull/6631/files. This fixes https://github.com/galaxyproject/galaxy/issues/6769 Commit: 70e325574cb82be62b1be8090e714ce44441686b https://github.com/galaxyproject/galaxy/commit/70e325574cb82be62b1be8090e71… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Use with statement for all file uploads Commit: 5a98515df88b68483ad59bb7208a57f1a7f71664 https://github.com/galaxyproject/galaxy/commit/5a98515df88b68483ad59bb7208a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-28 (Fri, 28 Sep 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools_upload.py Log Message: ----------- Merge pull request #6789 from mvdbeek/fix_bam_upload [18.09] Fix bam upload resulting in 'auto' datatype Compare: https://github.com/galaxyproject/galaxy/compare/c5a325d01535...5a98515df88b **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] 12f035: Main: mutable configs for Gemini install
by GitHub 28 Sep '18

28 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 12f035accb4d027ae548f415bdc89e1c07374a8f https://github.com/galaxyproject/usegalaxy-playbook/commit/12f035accb4d027a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-27 (Thu, 27 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_data_manager_conf.xml Log Message: ----------- Main: mutable configs for Gemini install **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] ed2d7a: Stop attempting to load broken and unusable report...
by GitHub 28 Sep '18

28 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 28 Sep '18

28 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 28 Sep '18

28 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 28 Sep '18

28 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 28 Sep '18

28 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 28 Sep '18

28 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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galaxy-commits September 2018