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

[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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