- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 7eb0be: Restore log_destination = stdout configuration opt...
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 7eb0be96cf3dba5099f28fd001c5f2b87ddacf38 https://github.com/galaxyproject/galaxy/commit/7eb0be96cf3dba5099f28fd001c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/config.py Log Message: ----------- Restore log_destination = stdout configuration option. Implementation in 17.09 was here https://github.com/galaxyproject/galaxy/blob/release_17.09/lib/galaxy/confi…. This option set to stdout is used by the test framework output Galaxy logs to stdout. As far as I can tell log_destination was removed in 18.01 and the effect was to sort of default to stdout - but when we fixed log_destination for files and backported recently https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d… - test output became written to a file called "stdout". This commit should restore the 17.09 behavior for both files and stdout configuration of this logging. Commit: 272c6b071d5c5db526cb3da8cc174dd4785a0d6e https://github.com/galaxyproject/galaxy/commit/272c6b071d5c5db526cb3da8cc17… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Test case to clarify workflow API a bit in simple cases. Commit: 9874e5db0cbf1967a90d3ad74820af1790602981 https://github.com/galaxyproject/galaxy/commit/9874e5db0cbf1967a90d3ad74820… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Allow uniform access to job state for WorkflowInvocationSteps. Use the concept of job_source_type and job_source_id used by IDs to summarize the state and list out individual jobs in the response as a shortcut. This information used to be readily accessible before 18.01. Commit: b878835ea388cc7ea15c0bf9d56738732d44b8e2 https://github.com/galaxyproject/galaxy/commit/b878835ea388cc7ea15c0bf9d567… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-08-08 (Wed, 08 Aug 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Add a legacy_job_state mode to restore 17.09 workflow invocation behavior. Commit: 71b561512db9819b68f9685d3e43317ba43790b2 https://github.com/galaxyproject/galaxy/commit/71b561512db9819b68f9685d3e43… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/config.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/workflows.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #6559 from jmchilton/wf_api_legacy [18.01] Restore the ability to track jobs for a WF invocation step. Compare: https://github.com/galaxyproject/galaxy/compare/7d7a875af398...71b561512db9 **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] f32989: Don't skip build on release/master moving forward.
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: f3298953d41cb0e2b37812242a88d226a890e8aa https://github.com/galaxyproject/galaxy/commit/f3298953d41cb0e2b37812242a88… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Don't skip build on release/master moving forward. Commit: bd5d12049b238c4475f267fbbf63bd3a124b0a58 https://github.com/galaxyproject/galaxy/commit/bd5d12049b238c4475f267fbbf63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Swap nodeenv to a pinned requirement. Commit: 4d6d984fbd8d66b30c7da3cd5022903f11218b09 https://github.com/galaxyproject/galaxy/commit/4d6d984fbd8d66b30c7da3cd5022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M client/README.md Log Message: ----------- Update client/README Commit: 3f8c2beff252587cd1347142ab84ad20afd57b03 https://github.com/galaxyproject/galaxy/commit/3f8c2beff252587cd1347142ab84… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-21 (Fri, 21 Sep 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Swap to a production w/ sourcemaps build by default for autobuilder (though, of course, folks can manually do whatever -- seems like the most sensible default though) Commit: eb1980ec087d7a2c3da6d138155f6c11895a8b26 https://github.com/galaxyproject/galaxy/commit/eb1980ec087d7a2c3da6d138155f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/README.md M lib/galaxy/dependencies/pipfiles/default/Pipfile M lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M scripts/common_startup.sh Log Message: ----------- Merge pull request #6753 from dannon/client-build-startup-changes [18.09] Client build startup changes Compare: https://github.com/galaxyproject/galaxy/compare/46dd1801cbc1...eb1980ec087d **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] 2d9b80: Use UserRoleAssociation to get private roles
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 2d9b803025828869c50a70db25fb7654caa17368 https://github.com/galaxyproject/galaxy/commit/2d9b803025828869c50a70db25fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Use UserRoleAssociation to get private roles If I understand this correctly this should work even if the user email changes. Commit: 5a97e4fcea77426eab0a7ca22402cdf8b638f79b https://github.com/galaxyproject/galaxy/commit/5a97e4fcea77426eab0a7ca22402… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Merge pull request #6771 from mvdbeek/fix_private_role_none [18.05] Use UserRoleAssociation to get private roles Compare: https://github.com/galaxyproject/galaxy/compare/02c177152bd7...5a97e4fcea77 **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] 60c416: Fix unit tests that access output label
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 60c4162ffafdbdb8b741d01b472d271910025de5 https://github.com/galaxyproject/galaxy/commit/60c4162ffafdbdb8b741d01b472d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Fix unit tests that access output label Commit: cb5b054aa0c995d106ea9dff12fbade43c9233a1 https://github.com/galaxyproject/galaxy/commit/cb5b054aa0c995d106ea9dff12fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M test/unit/workflows/test_modules.py Log Message: ----------- Merge branch 'display_label_in_wf' of https://github.com/mvdbeek/galaxy into display_label_in_wf Compare: https://github.com/galaxyproject/galaxy/compare/7bb0c3904c4f...cb5b054aa0c9 **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] 4cdd07: Display output label in workflow editor if present
by GitHub 26 Sep '18

26 Sep '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4cdd0774c5fd5b9a1eaafe034ae1c20c077abf92 https://github.com/galaxyproject/galaxy/commit/4cdd0774c5fd5b9a1eaafe034ae1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-25 (Tue, 25 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view-data.js M lib/galaxy/workflow/modules.py Log Message: ----------- Display output label in workflow editor if present Commit: ba7c5a7162cffd13ff61201a4d2346e9b1b55afb https://github.com/galaxyproject/galaxy/commit/ba7c5a7162cffd13ff61201a4d23… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Display labels in output actions This displays the output label (if available) in the output section, for instance `Configure Output: 'Table split on column'` instead of `Configure Output: 'out1'`, and it displays available input variables as a list in the Rename dataset section, with the label next to the variable name. Commit: 7bb0c3904c4fe00ae3a8294088717b2de74d7462 https://github.com/galaxyproject/galaxy/commit/7bb0c3904c4fe00ae3a829408871… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-09-26 (Wed, 26 Sep 2018) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M client/galaxy/scripts/mvc/ui/ui-list.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-popover.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/upload-settings.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/ui.scss M client/galaxy/style/scss/upload.scss Log Message: ----------- Client format re-sync. Compare: https://github.com/galaxyproject/galaxy/compare/66c6c84c4d61...7bb0c3904c4f **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] 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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[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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