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

[galaxyproject/usegalaxy-playbook] 27e5bf: Typo
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 27e5bf6f85dda6f60a2da6141f2051388af20151 https://github.com/galaxyproject/usegalaxy-playbook/commit/27e5bf6f85dda6f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Typo **NOTE:** This service 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] a21f73: Enable temporary reserved partition on JS@IU
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a21f73c5204b03d028c8717f1678e04af7e79c3c https://github.com/galaxyproject/usegalaxy-playbook/commit/a21f73c5204b03d0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Enable temporary reserved partition on JS@IU **NOTE:** This service 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] fe57bc: Add a temporary reserved partition to JS@IU
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fe57bc88a4cd6b53ee5dfa19db16d87ff2bd13d9 https://github.com/galaxyproject/infrastructure-playbook/commit/fe57bc88a4c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/jsiu/templates/slurm/slurm.conf.j2 Log Message: ----------- Add a temporary reserved partition to JS@IU **NOTE:** This service 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] e4b242: Update Main
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e4b2426fe1511f02d4c017a6a16cab4be6224da8 https://github.com/galaxyproject/usegalaxy-playbook/commit/e4b2426fe1511f02… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **NOTE:** This service 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] 676886: Fix non-strict tabular relabel operation
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 676886195d1fbe17cdff16af8acad6f5c2115ee1 https://github.com/galaxyproject/galaxy/commit/676886195d1fbe17cdff16af8aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix non-strict tabular relabel operation Commit: 3b3deb314f4a78684bea9707d2f0d856e306f006 https://github.com/galaxyproject/galaxy/commit/3b3deb314f4a78684bea9707d2f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Use strict mode when testing strict mode ... Commit: 470299a2ce6ef1e5d894a0247bd43f24fd463d41 https://github.com/galaxyproject/galaxy/commit/470299a2ce6ef1e5d894a0247bd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Merge pull request #6234 from mvdbeek/fix_relabel_non_strict [18.01] Fix non-strict tabular relabel operation Commit: eed703eef8b3884f70019070210633f0e033b39b https://github.com/galaxyproject/galaxy/commit/eed703eef8b3884f700190702106… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix share with another user in 18.05 Commit: 48fafa8096fd179e9c74c56bac7be9b042cbade8 https://github.com/galaxyproject/galaxy/commit/48fafa8096fd179e9c74c56bac7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Merge pull request #6358 from dannon/1805sharingfix [18.01] Fix 'share with another user' Commit: d0a0fa8319e5b32e222e261b1b9f0242e210d1c7 https://github.com/galaxyproject/galaxy/commit/d0a0fa8319e5b32e222e261b1b9f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml M templates/sharing_base.mako Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: f89c6a40820756a32087c611771b4a466ffca39e https://github.com/galaxyproject/galaxy/commit/f89c6a40820756a32087c611771b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f9ba72f0aecb...f89c6a408207 **NOTE:** This service 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] 676886: Fix non-strict tabular relabel operation
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 676886195d1fbe17cdff16af8acad6f5c2115ee1 https://github.com/galaxyproject/galaxy/commit/676886195d1fbe17cdff16af8aca… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-28 (Mon, 28 May 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix non-strict tabular relabel operation Commit: 3b3deb314f4a78684bea9707d2f0d856e306f006 https://github.com/galaxyproject/galaxy/commit/3b3deb314f4a78684bea9707d2f0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Use strict mode when testing strict mode ... Commit: 470299a2ce6ef1e5d894a0247bd43f24fd463d41 https://github.com/galaxyproject/galaxy/commit/470299a2ce6ef1e5d894a0247bd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml Log Message: ----------- Merge pull request #6234 from mvdbeek/fix_relabel_non_strict [18.01] Fix non-strict tabular relabel operation Commit: eed703eef8b3884f70019070210633f0e033b39b https://github.com/galaxyproject/galaxy/commit/eed703eef8b3884f700190702106… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Fix share with another user in 18.05 Commit: 48fafa8096fd179e9c74c56bac7be9b042cbade8 https://github.com/galaxyproject/galaxy/commit/48fafa8096fd179e9c74c56bac7b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M templates/sharing_base.mako Log Message: ----------- Merge pull request #6358 from dannon/1805sharingfix [18.01] Fix 'share with another user' Commit: d0a0fa8319e5b32e222e261b1b9f0242e210d1c7 https://github.com/galaxyproject/galaxy/commit/d0a0fa8319e5b32e222e261b1b9f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/relabel_from_file.xml M templates/sharing_base.mako Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/bcf105cbb37a...d0a0fa8319e5 **NOTE:** This service 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] bcc38c: Tool updates and installations:
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bcc38ca365f66914800b82fbed2aaa47e078bc11 https://github.com/galaxyproject/usegalaxy-playbook/commit/bcc38ca365f66914… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_data_manager_conf.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: ----------- Tool updates and installations: - length_and_gc_content v0.1.1 - trimmomatic v0.36.5 - deeptools_bam_coverage v3.0.2.0 - salmon v0.9.1 - kallisto_quant v0.43.1.3 - kallisto_pseudo v0.43.1.1 - sailfish v0.10.1.1 - limma_voom v3.34.9.7 - edger v3.20.7.2 - goseq v1.26.0 - deseq2 v2.11.40.2 - featurecounts v1.6.0.6 - tophat2 v2.1.1 - stringtie v1.3.3.2 - ggplot2_heatmap2 v2.2.1+galaxy0 - rseqc_deletion_profile v2.6.4 - rseqc_geneBody_coverage2 v2.6.4.1 - rseqc_RPKM_saturation v2.6.4.1 - rseqc_infer_experiment v2.6.4.1 - rseqc_read_NVC v2.6.4 - rseqc_RNA_fragment_size v2.6.4.1 - rseqc_geneBody_coverage v2.6.4.2 - rseqc_bam_stat v2.6.4 - rseqc_tin v2.6.4.1 - rseqc_read_duplication v2.6.4 - rseqc_junction_saturation v2.6.4.1 - rseqc_read_GC v2.6.4 - rseqc_insertion_profile v2.6.4 - rseqc_bam2wig v2.6.4 - rseqc_FPKM_count v2.6.4.1 - rseqc_read_distribution v2.6.4.1 - rseqc_clipping_profile v2.6.4 - rseqc_read_quality v2.6.4 - rseqc_read_hexamer v2.6.4 - rseqc_mismatch_profile v2.6.4 - rseqc_junction_annotation v2.6.4.1 - rseqc_inner_distance v2.6.4.1 **NOTE:** This service 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] 486a63: Run hifive in multi partition
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 486a6392538dad3dada4796fdcf36e927e3f5b7f https://github.com/galaxyproject/usegalaxy-playbook/commit/486a6392538dad3d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run hifive in multi partition **NOTE:** This service 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] 89f4ee: Fix Jetstream concurrency limits
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 89f4eecaf38b84ebda1b0a639f46a221f95cbc09 https://github.com/galaxyproject/usegalaxy-playbook/commit/89f4eecaf38b84eb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Fix Jetstream concurrency limits Commit: 2eeb255617f3123aa9ccf30e1d573e6633f8d833 https://github.com/galaxyproject/usegalaxy-playbook/commit/2eeb255617f3123a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py A env/test/files/galaxy/dynamic_rules/multi_dynamic_walltime.py R env/test/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Logging fix for the main dynamic rule Commit: 4f577662ba7c927bd49fce54529586bdac2142a2 https://github.com/galaxyproject/usegalaxy-playbook/commit/4f577662ba7c927b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Use --cpus-per-task rather than --ntasks, and don't set --mem-per-cpu on multi, as the partition defaults will set this correctly. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/15ce8c98ba3c...… **NOTE:** This service 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] 71a08a: Handle instance launch failures
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 71a08ae93d6fd3035f9be01c72d7cb742d4c750b https://github.com/galaxyproject/infrastructure-playbook/commit/71a08ae93d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M roles/slurmscale/files/resume.yml Log Message: ----------- Handle instance launch failures Commit: 0bccefe140370fc12d41db7a25f78c249ae24db7 https://github.com/galaxyproject/infrastructure-playbook/commit/0bccefe1403… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M roles/slurmscale/templates/suspend_resume.sh.j2 Log Message: ----------- Improve logging for slurm suspend/resume script, plus fix a bug whereby the log file name was too long when launching many instances at once. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/1032dfe139… **NOTE:** This service 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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