- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] d4acd9: The great repository upgrade project.
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d4acd9b118e413adb35bdf059c8c987d1c75b290 https://github.com/galaxyproject/usegalaxy-playbook/commit/d4acd9b118e413ad… 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. - text_processing v1.1.1 - count_gff_features v0.2 Commit: 1f9cf764d892916886ea3b6695e44fca67b0316f https://github.com/galaxyproject/usegalaxy-playbook/commit/1f9cf764d8929168… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Upgrade gemini tools to 0.18.1 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/73a78cbea11d...… **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] 300d31: Resilience of success message handling
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 300d316ad1bcd0ec1a7b762e859232bbe8c9548c https://github.com/galaxyproject/galaxy/commit/300d316ad1bcd0ec1a7b762e8592… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Resilience of success message handling Commit: 46dd1801cbc11cb24bb7fdd0d8a4f8e71fa9ef9e https://github.com/galaxyproject/galaxy/commit/46dd1801cbc11cb24bb7fdd0d8a4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #6768 from martenson/backport_resilience_of_success_message_handling [18.09] backport of: Resilience of success message handling Compare: https://github.com/galaxyproject/galaxy/compare/9f688b2f9141...46dd1801cbc1 **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] 73a78c: 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: 73a78cbea11d3cc23ffa339846db3f730fa9cd89 https://github.com/galaxyproject/usegalaxy-playbook/commit/73a78cbea11d3cc2… 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. - stringtie v1.3.4 - limma_voom v3.34.9.8 - hisat2 v2.1.0 - samtools_sort v2.0.2 - samtools_mpileup v2.1.4 - samtools_flagstat v2.0.1 - samtool_filter2 v1.8 - bam_to_sam v2.0.1 - vcfdistance v1.0.0_rc1 - varscan v2.4.2 - snpeff v4.3+T **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] b75a7c: Send 404s to logflux without intercepting them
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b75a7cc5ae5808a54dcc8586dbd8758ee68285bd https://github.com/galaxyproject/usegalaxy-playbook/commit/b75a7cc5ae5808a5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Send 404s to logflux without intercepting them **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] bc6e86: Add logflux config to catch 404s on Test
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bc6e86ff75895fb6b885f9354b69666f229b7353 https://github.com/galaxyproject/usegalaxy-playbook/commit/bc6e86ff75895fb6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/test/group_vars/logfluxservers.yml M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Add logflux config to catch 404s on Test **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] 35984d: Update access list
by GitHub 25 Sep '18

25 Sep '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 35984d8b3a411a25d0c969a315fd328ea4ff58ec https://github.com/galaxyproject/infrastructure-playbook/commit/35984d8b3a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M env/galaxy/host_vars/orval.galaxyproject.org/vault.yml Log Message: ----------- Update access list **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] 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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