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

[galaxyproject/galaxy] 6ddcc9: Add py34-unit (allowed to fail) job to Travis
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ddcc9340d5a36497642339c52c2e3e4cb0fca67 https://github.com/galaxyproject/galaxy/commit/6ddcc9340d5a36497642339c52c2… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Add py34-unit (allowed to fail) job to Travis Commit: e49ee433e82a31f4d0560bb4727cd5b80aefd8e9 https://github.com/galaxyproject/galaxy/commit/e49ee433e82a31f4d0560bb4727c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Speedup the py34-first_startup TravisCI job By skipping most database migrations, as for py27-first_startup. Commit: 02e7734868df8e9a7d3e8583e163ba13694764d0 https://github.com/galaxyproject/galaxy/commit/02e7734868df8e9a7d3e8583e163… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-29 (Fri, 29 Jun 2018) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #6406 from nsoranzo/py34-unit_on_travis Add py34-unit (allowed to fail) job to Travis Compare: https://github.com/galaxyproject/galaxy/compare/2b55e3a09962...02e7734868df **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] bd52ea: Install Seqtk 1.2
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd52ea967973d6deb8de057ba918d6fcb8889f53 https://github.com/galaxyproject/usegalaxy-playbook/commit/bd52ea967973d6de… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-29 (Fri, 29 Jun 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: ----------- Install Seqtk 1.2 **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] 5202d3: Set up starforge user for travis
by GitHub 29 Jun '18

29 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5202d3cc77c9c496ca48d266fd235a259de59daa https://github.com/galaxyproject/infrastructure-playbook/commit/5202d3cc77c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-28 (Thu, 28 Jun 2018) Changed paths: M env/galaxy/group_vars/sshclients/vault.yml M env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vault.yml Log Message: ----------- Set up starforge user for travis **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] 882517: Installed version 0.5.4 of pRESTO.
by GitHub 27 Jun '18

27 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8825178e89a49d611e92a5a01606dbaf8324c6d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/8825178e89a49d61… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-27 (Wed, 27 Jun 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: ----------- Installed version 0.5.4 of pRESTO. **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] c44328: Rewrite admin data types as vue component
by GitHub 27 Jun '18

27 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c4432865124375c8e437e81f92e6667121c9beb6 https://github.com/galaxyproject/galaxy/commit/c4432865124375c8e437e81f92e6… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/components/admin/DataTypes.vue M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Rewrite admin data types as vue component Take the DataTables component as an example and do the same for data types. - Add DataTypes vue component which reuses BaseGrid and Message - Users have the option to show predefined or all columns supplied by the api - Add data_types_list web api which returns all datatypes and their attributes - Add client route for admin/data_types and reflect the change in admin router Commit: 1bff38c68536e7856ef9a7e33e825e804a5d6ee4 https://github.com/galaxyproject/galaxy/commit/1bff38c68536e7856ef9a7e33e82… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Fix whitespace Commit: b4814bb1b10579b059ae89de58d149a6f472b355 https://github.com/galaxyproject/galaxy/commit/b4814bb1b10579b059ae89de58d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/view_datatypes_registry.mako Log Message: ----------- Remove datatpes registry template/endpoint (previous commit replaces this functionality on the client side). Commit: ae81a1444cb5afd284da89c3ca192f7c5f9ef2a1 https://github.com/galaxyproject/galaxy/commit/ae81a1444cb5afd284da89c3ca19… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/layout/data.js Log Message: ----------- Client format Commit: 2b55e3a099624fa54fcfb9b7276713764d282b8c https://github.com/galaxyproject/galaxy/commit/2b55e3a099624fa54fcfb9b72767… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/components/admin/DataTypes.vue M client/galaxy/scripts/layout/data.js M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py R templates/admin/view_datatypes_registry.mako Log Message: ----------- Merge branch 'admin.data.types.vue' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a13bcd1f9710...2b55e3a09962 **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] b22459: Update dev dependencies
by GitHub 27 Jun '18

27 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b22459871ba40140f03c799211d3e000366eb8fc https://github.com/galaxyproject/galaxy/commit/b22459871ba40140f03c799211d3… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-26 (Tue, 26 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock Log Message: ----------- Update dev dependencies In particular for NoseHTML 0.4.5, which will enable unit testing under Python 3. Commit: a13bcd1f9710a5017ce13f68d194a7f50b3f4bd0 https://github.com/galaxyproject/galaxy/commit/a13bcd1f9710a5017ce13f68d194… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-27 (Wed, 27 Jun 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock Log Message: ----------- Merge pull request #6403 from nsoranzo/update_dev_deps Update dev dependencies Compare: https://github.com/galaxyproject/galaxy/compare/11b266344c46...a13bcd1f9710 **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] 8fb738: Add a redirect for my slides
by GitHub 27 Jun '18

27 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8fb7387445dd0d905701b959eaeb76b2ea1bfecc https://github.com/galaxyproject/infrastructure-playbook/commit/8fb7387445d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-26 (Tue, 26 Jun 2018) Changed paths: M env/galaxy/templates/nginx/gxy.io.j2 Log Message: ----------- Add a redirect for my slides **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] 6b627f: Allow resource selection for data managers
by GitHub 26 Jun '18

26 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6b627fc40fb62afc72e43eb9abb3fd3c3158c148 https://github.com/galaxyproject/galaxy/commit/6b627fc40fb62afc72e43eb9abb3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Allow resource selection for data managers We used to restrict this to standard tools, but there's no reason why this shouldn't work for data manager tools. Fixes https://github.com/galaxyproject/galaxy/issues/6396 Commit: 11b266344c46fbfbd90fb3cd6ace4fd8a5923bf5 https://github.com/galaxyproject/galaxy/commit/11b266344c46fbfbd90fb3cd6ace… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-26 (Tue, 26 Jun 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6402 from mvdbeek/resource_selection_data_manager_tools Allow resource selection for data managers Compare: https://github.com/galaxyproject/galaxy/compare/ed6f5d45a9ec...11b266344c46 **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] 35423a: Serve singularity images with rsync
by GitHub 25 Jun '18

25 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 35423adc74455d796074c72d2428dcbe93037b2a https://github.com/galaxyproject/infrastructure-playbook/commit/35423adc744… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml Log Message: ----------- Serve singularity images with rsync **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] 021c8f: Fixing <conditional> XML example
by GitHub 25 Jun '18

25 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 021c8f0bd8e6582ee6e671f7e20b5786f224f11e https://github.com/galaxyproject/galaxy/commit/021c8f0bd8e6582ee6e671f7e20b… Author: Alexandru Mahmoud <amahmou4(a)jhu.edu> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Fixing <conditional> XML example Commit: ed6f5d45a9ecbf0cf8a85341e0213b82a9132a46 https://github.com/galaxyproject/galaxy/commit/ed6f5d45a9ecbf0cf8a85341e021… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-25 (Mon, 25 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6399 from almahmoud/dev Fixing <conditional> XML example Compare: https://github.com/galaxyproject/galaxy/compare/fbb032f4e1b0...ed6f5d45a9ec **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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