- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy]
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/blank_log_lines Home: https://github.com/galaxyproject/galaxy **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] 661ad9: Remove empty log messages
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 661ad9bd1ef5562b23f542eb40dc4f42b488f1bf https://github.com/galaxyproject/galaxy/commit/661ad9bd1ef5562b23f542eb40dc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove empty log messages e.g. ``` galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,006 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_hcluster/mothur_hcluster/1.36.1.0, version: 1.36.1.0 into tool panel.... galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,012 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 ``` Commit: eaa1211e474943838988d6ceec3e38111cb59236 https://github.com/galaxyproject/galaxy/commit/eaa1211e474943838988d6ceec3e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Cleaner check for log message Commit: 66c6c84c4d61a504d0aefe0cadceef0dffad2c74 https://github.com/galaxyproject/galaxy/commit/66c6c84c4d61a504d0aefe0cadce… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #6763 from galaxyproject/blank_log_lines Remove empty log messages Compare: https://github.com/galaxyproject/galaxy/compare/9062363c4320...66c6c84c4d61 **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] eaa121: Cleaner check for log message
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/blank_log_lines Home: https://github.com/galaxyproject/galaxy Commit: eaa1211e474943838988d6ceec3e38111cb59236 https://github.com/galaxyproject/galaxy/commit/eaa1211e474943838988d6ceec3e… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Cleaner check for log message **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] 661ad9: Remove empty log messages
by GitHub 24 Sep '18

24 Sep '18

Branch: refs/heads/blank_log_lines Home: https://github.com/galaxyproject/galaxy Commit: 661ad9bd1ef5562b23f542eb40dc4f42b488f1bf https://github.com/galaxyproject/galaxy/commit/661ad9bd1ef5562b23f542eb40dc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-24 (Mon, 24 Sep 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Remove empty log messages e.g. ``` galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,005 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,006 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,007 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,008 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_hcluster/mothur_hcluster/1.36.1.0, version: 1.36.1.0 into tool panel.... galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,009 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,010 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,011 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,012 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,013 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 galaxy.tools.toolbox.base DEBUG 2018-09-25 03:21:20,014 ``` **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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