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

[galaxyproject/usegalaxy-playbook] 1e00ae: Update Main
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e00ae892139ef2ae9330ae30a6ef772a0a19a52 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e00ae892139ef2a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **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] 0698a7: Another few stragglers.
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/18.09_release_notes Home: https://github.com/galaxyproject/galaxy Commit: 0698a71861afadb7f16be765223819178d294c30 https://github.com/galaxyproject/galaxy/commit/0698a71861afadb7f16be7652238… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Another few stragglers. Commit: d3db21fa82a834d0d9fa90106b3fa2b4911708dc https://github.com/galaxyproject/galaxy/commit/d3db21fa82a834d0d9fa90106b3f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Add 6755 Compare: https://github.com/galaxyproject/galaxy/compare/6ac5966c5e1a...d3db21fa82a8 **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] 679603: Catch any failures encountered while pausing/stopp...
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 679603b7c9a2b1f8c136dcc29d2eb41174bd6b31 https://github.com/galaxyproject/galaxy/commit/679603b7c9a2b1f8c136dcc29d2e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok, so that it doesn't interrupt processing other jobs. That was discovered because attempting to delete purged job outputs on failure was raising ObjectNotFound since dataset object store assignment is done later now. So also, catch that ObjectNotFound. Commit: 9f688b2f9141683e02ea9aa759a15ebd46174042 https://github.com/galaxyproject/galaxy/commit/9f688b2f9141683e02ea9aa759a1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6755 from natefoo/job-object-store-fixes [18.09] Catch any failures encountered while pausing/stopping jobs whose inputs are terminal and non-ok Compare: https://github.com/galaxyproject/galaxy/compare/529ed61c3b48...9f688b2f9141 **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] de6dc0: Don't attempt len(None), ensure stdout/stderr are ...
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: de6dc00236ad2947d3bef479b5d7df5c3bef7ba4 https://github.com/galaxyproject/galaxy/commit/de6dc00236ad2947d3bef479b5d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Commit: 529ed61c3b48e2d8a830e6a890d93b16a4f42ea4 https://github.com/galaxyproject/galaxy/commit/529ed61c3b48e2d8a830e6a890d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #6765 from natefoo/job-stdout-none-fix [18.09] Don't attempt len(None), ensure stdout/stderr are strings in Job(Like).set_streams(). Compare: https://github.com/galaxyproject/galaxy/compare/a89184aa707a...529ed61c3b48 **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] a0ad5a: Increase the maximum number of stderr lines that w...
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: a0ad5adf6fc02c6a0864308f8d6f8a612a83f308 https://github.com/galaxyproject/galaxy/commit/a0ad5adf6fc02c6a0864308f8d6f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Increase the maximum number of stderr lines that will be scanned for slurm warnings to strip to 3. Commit: a89184aa707a477f14905bd44b368006c7cae427 https://github.com/galaxyproject/galaxy/commit/a89184aa707a477f14905bd44b36… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6766 from natefoo/remove-more-slurm-warnings [18.09] Increase the maximum number of stderr lines that will be scanned for slurm warnings Compare: https://github.com/galaxyproject/galaxy/compare/ea7359b08b21...a89184aa707a **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] e5e97d: The great repository upgrade project.
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e5e97dc302bfaa157937bfd9f59bf9fe728d7259 https://github.com/galaxyproject/usegalaxy-playbook/commit/e5e97dc302bfaa15… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- The great repository upgrade project. - pear v0.9.6.1 - salmon v0.11.2 - diamond v0.8.24 **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/infrastructure-playbook] b3e47b: Forgot sinfo could format properly for pdsh itself
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b3e47b6f59b81edc09977bb5444f4e7db95401d8 https://github.com/galaxyproject/infrastructure-playbook/commit/b3e47b6f59b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/jscommon/files/admin/pdsh-up Log Message: ----------- Forgot sinfo could format properly for pdsh itself **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] 58f66b: The great repository upgrade project.
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 58f66b43a575575de1ae7f6654056b2aa1d8f7ac https://github.com/galaxyproject/usegalaxy-playbook/commit/58f66b43a575575d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- The great repository upgrade project. - multiqc v1.6 - flash v1.2.11.3 - fastx_trimmer v1.0.2 - fastx_reverse_complement v1.0.2 - fastx_clipper v1.0.3 - fastq_quality_filter v1.0.2 **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] ebf017: Add a wrapper for pdsh to pdsh Jetstream nodes tha...
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: ebf017b2c19355113d91e6e7ed35efd0da3ed4a8 https://github.com/galaxyproject/infrastructure-playbook/commit/ebf017b2c19… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: A env/jscommon/files/admin/pdsh-up M env/jscommon/group_vars/controllers.yml M env/jsiu/playbook.yml Log Message: ----------- Add a wrapper for pdsh to pdsh Jetstream nodes that are up **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] 16d7de: Update rgWebLogo3 to v3.5.0
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 16d7de12d9f11a4c0d58f825a4844cd713743237 https://github.com/galaxyproject/usegalaxy-playbook/commit/16d7de12d9f11a4c… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update rgWebLogo3 to v3.5.0 Commit: e7f2683342042282c40c564a2b92c3d75d2a93bf https://github.com/galaxyproject/usegalaxy-playbook/commit/e7f2683342042282… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- The great repository upgrade project. - ngsutils_bam_filter v0.5.9 - macs2 v2.1.1.20160309 - unicycler v0.4.6 - prokka v1.13 - meme_meme v4.12.0 - meme_fimo v4.12.0 - weblogo3 v3.5.0 - genetrack v1.0.1 - bamtools_split v2.4.0 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a3f69979a7b6...… **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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