- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 6cf034: Some style cleanup.
by GitHub 24 Jun '18

24 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6cf034ef6f6c67c6464cd85d7adc5f2ecaaa9452 https://github.com/galaxyproject/galaxy/commit/6cf034ef6f6c67c6464cd85d7adc… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/styleguide.config.js M client/yarn.lock M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Some style cleanup. - Split the Galaxy components of the styleguide into multiple documents to make things more manageable and get a better table of contents. Add some additional examples for masthead and panels. - Use flexbox for layout of panels and masthead. This eliminates a lot of absolute positioning from the panels and allows the masthead and panel headers to layour correctly regardles of height. - Unify the set of gray levels we are using (to those from Bootstrap 4) - Add some additional SCSS variables and (small amount of) general cleanup to styles. Commit: db3739fcfe8217493f648d3e06390071b12fa217 https://github.com/galaxyproject/galaxy/commit/db3739fcfe8217493f648d3e0639… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Position masthead/scratchbook sub icons Commit: f16da195c58a9ac157c85db4369bc28a5089fd43 https://github.com/galaxyproject/galaxy/commit/f16da195c58a9ac157c85db4369b… Author: James Taylor <james(a)jamestaylor.org> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #6 from guerler/ui-flex-scratchbook Fixes the position of small sub-icons in masthead Commit: fbb032f4e1b0a6239ced4e7753a0f8156abf3e85 https://github.com/galaxyproject/galaxy/commit/fbb032f4e1b0a6239ced4e7753a0… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-24 (Sun, 24 Jun 2018) Changed paths: A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md R client/galaxy/docs/galaxy-styles.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/galaxy_bootstrap/variables.scss M client/galaxy/style/scss/galaxy_variables.scss M client/galaxy/style/scss/theme/blue.scss M client/galaxy/style/scss/upload.scss M client/package.json M client/styleguide.config.js M client/yarn.lock M templates/base/base_panels.mako M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6386 from jxtx/ui-flex Some style cleanup. Compare: https://github.com/galaxyproject/galaxy/compare/31e78461bd1e...fbb032f4e1b0 **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/ansible-galaxy]
by GitHub 23 Jun '18

23 Jun '18

Branch: refs/tags/0.7.6 Home: https://github.com/galaxyproject/ansible-galaxy **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/ansible-galaxy] 8417a5: Switch to Ansible 2.4 dynamic task includes to avo...
by GitHub 23 Jun '18

23 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 8417a5bf92da86c1fd1d8e19dce86c9eaf675701 https://github.com/galaxyproject/ansible-galaxy/commit/8417a5bf92da86c1fd1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M meta/main.yml M tasks/dependencies.yml M tasks/download.yml M tasks/main.yml Log Message: ----------- Switch to Ansible 2.4 dynamic task includes to avoid tons of skips when running the role in pieces. Commit: 719fa075397f562fb7c14bdb2f71d911c24fa527 https://github.com/galaxyproject/ansible-galaxy/commit/719fa075397f562fb7c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A .gitignore M README.md M defaults/main.yml A filter_plugins/uwsgi_yaml.py M tasks/clone.yml M tasks/errordocs.yml M tasks/static_setup.yml M templates/galaxy.ini.j2 A templates/galaxy.yml.j2 Log Message: ----------- Support for YAML galaxy config Commit: b3a7689137fedfc50d101febd9896545125d71cb https://github.com/galaxyproject/ansible-galaxy/commit/b3a7689137fedfc50d10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M README.md Log Message: ----------- Clarify the uWSGI YAML syntax and provide an example Commit: b69cc10a46132de4dff6172ab112bf2192aad740 https://github.com/galaxyproject/ansible-galaxy/commit/b69cc10a46132de4dff6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M README.md Log Message: ----------- Give an example of starting job handler mules Commit: fa0df02a3eaf6399392a9ae22bf0913344ee6ebe https://github.com/galaxyproject/ansible-galaxy/commit/fa0df02a3eaf6399392a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: A .gitignore M README.md M defaults/main.yml A filter_plugins/uwsgi_yaml.py M meta/main.yml M tasks/clone.yml M tasks/dependencies.yml M tasks/download.yml M tasks/errordocs.yml M tasks/main.yml M tasks/static_setup.yml M templates/galaxy.ini.j2 A templates/galaxy.yml.j2 Log Message: ----------- Merge pull request #28 from galaxyproject/yaml-uwsgi uWSGI/Galaxy YAML config support Compare: https://github.com/galaxyproject/ansible-galaxy/compare/a8a01bb5fe0d...fa0d… **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] c6403a: Fix logging bug.
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c6403acd0f18196c0453a90fe89ccf861d7a28d6 https://github.com/galaxyproject/galaxy/commit/c6403acd0f18196c0453a90fe89c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix logging bug. Commit: 6d5be41b320510d6e2d163399a3a6e30d6f9bda0 https://github.com/galaxyproject/galaxy/commit/6d5be41b320510d6e2d163399a3a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6366 from jmchilton/job_log_bug [18.05] Fix small bug in logging output name in job finish. Commit: 572f38d1fb47e914ad10766007c855786e1643a2 https://github.com/galaxyproject/galaxy/commit/572f38d1fb47e914ad10766007c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- move the sanitization to the try/except block as it may fail (and it did, on Main) Commit: d28ab2a4f31b363c236a02a535cc43ab049190ca https://github.com/galaxyproject/galaxy/commit/d28ab2a4f31b363c236a02a535cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6377 from martenson/catch-sanitization-faults [18.05] Catch sanitization faults Commit: 9967639bac92eb3f7103794663f41b88f11baa9c https://github.com/galaxyproject/galaxy/commit/9967639bac92eb3f7103794663f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Comma-separate tool names in missing tools error message Commit: 22d383c39842e0a0198cf2d37ad3832ea1838769 https://github.com/galaxyproject/galaxy/commit/22d383c39842e0a0198cf2d37ad3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6378 from guerler/commaseperror [18.05] Comma-separate tool names in missing tools error message Commit: fa2b6baef71984c0559c53ff5750d1fe9b77163e https://github.com/galaxyproject/galaxy/commit/fa2b6baef71984c0559c53ff5750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Revert "Remove bam to bai converter" This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb. Commit: 5f24794efdad757b77c75c3aa111da7a11c5bb47 https://github.com/galaxyproject/galaxy/commit/5f24794efdad757b77c75c3aa111… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add basic .bai datatype Commit: 36706e9eb38728c91c1da2a4cf66ff49f3f44d72 https://github.com/galaxyproject/galaxy/commit/36706e9eb38728c91c1da2a4cf66… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #6385 from dannon/revert-baiconverter-removal [18.01] Revert "Remove bam to bai converter" Commit: e0c269291a20ae3a01a24bae930012baba3bb10c https://github.com/galaxyproject/galaxy/commit/e0c269291a20ae3a01a24bae9300… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 31e78461bd1e61ca8cc3dcdf0b6e08500b8ee2f1 https://github.com/galaxyproject/galaxy/commit/31e78461bd1e61ca8cc3dcdf0b6e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml M lib/galaxy/managers/workflows.py M lib/galaxy/tools/parameters/output_collect.py M scripts/grt/export.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/04b69d399b70...31e78461bd1e **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] fa2b6b: Revert "Remove bam to bai converter"
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fa2b6baef71984c0559c53ff5750d1fe9b77163e https://github.com/galaxyproject/galaxy/commit/fa2b6baef71984c0559c53ff5750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Revert "Remove bam to bai converter" This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb. Commit: 5f24794efdad757b77c75c3aa111da7a11c5bb47 https://github.com/galaxyproject/galaxy/commit/5f24794efdad757b77c75c3aa111… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add basic .bai datatype Commit: 36706e9eb38728c91c1da2a4cf66ff49f3f44d72 https://github.com/galaxyproject/galaxy/commit/36706e9eb38728c91c1da2a4cf66… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #6385 from dannon/revert-baiconverter-removal [18.01] Revert "Remove bam to bai converter" Commit: e0c269291a20ae3a01a24bae930012baba3bb10c https://github.com/galaxyproject/galaxy/commit/e0c269291a20ae3a01a24bae9300… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-23 (Sat, 23 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/22d383c39842...e0c269291a20 **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] a701a7: More correct, more efficient collection operations...
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a701a718a0c7675f21a063b225aa31cc54a0d4b4 https://github.com/galaxyproject/galaxy/commit/a701a718a0c7675f21a063b225aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py Log Message: ----------- More correct, more efficient collection operations. We were copying datasets and not assigning them new HIDs in some cases (the newer collection operations apply_rules, tag_from_file were doing the right thing here but it looks like we didn't go back and fix older operations). With the uniform handling of dataset copying in place - I used the much more efficient history.add_datasets instead of history.add_dataset. This also optimizes the actual HDA copying by eliminating some extra flushes. hda.copy() would flush to get an HDA before copying metadata but this is only needed if there are FileParameter metadata types (e.g. bams) so I made that flush conditional as well as the final one. So for most datatypes - this eliminates two extra flushes per dataset copied. Rebased with fix for issue pointed out by @nsoranzo - cleaned up _add_datasets_to_history to just consume values directly. Using itervalues since these methods have performance issues and these lists can be quite large. Commit: db5b368668265a5fcbd147d9db76cc64156bb6f7 https://github.com/galaxyproject/galaxy/commit/db5b368668265a5fcbd147d9db76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Don't rely on the order of history contents in test_map_over_collection_structured_like Commit: a10aab8f4f59d12c0d97fd45f1625576287e4a48 https://github.com/galaxyproject/galaxy/commit/a10aab8f4f59d12c0d97fd45f162… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove copy-paste mistakes. Commit: db036c6f51e53b537d6b88e872c2ecae74b72b44 https://github.com/galaxyproject/galaxy/commit/db036c6f51e53b537d6b88e872c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Another typo fix. Commit: 04b69d399b708aaab5b4166acfae89924cf8af7e https://github.com/galaxyproject/galaxy/commit/04b69d399b708aaab5b4166acfae… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/model/metadata.py M lib/galaxy/tools/__init__.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6370 from jmchilton/collection_operations_opt More correct, more efficient collection operations. Compare: https://github.com/galaxyproject/galaxy/compare/704f956306bb...04b69d399b70 **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] 6815ad: change a file read to use with statement
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6815ad69f4e5e7cf5ce8456d60a2325a682e52f6 https://github.com/galaxyproject/galaxy/commit/6815ad69f4e5e7cf5ce8456d60a2… Author: Qiang Gu <guqiang01(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- change a file read to use with statement Commit: 704f956306bb8a53e8697fac1ca536e53d2c1713 https://github.com/galaxyproject/galaxy/commit/704f956306bb8a53e8697fac1ca5… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #6388 from qiagu/data_column_1 change a file read to use with statement Compare: https://github.com/galaxyproject/galaxy/compare/d64bae64580e...704f956306bb **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] fa2b6b: Revert "Remove bam to bai converter"
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fa2b6baef71984c0559c53ff5750d1fe9b77163e https://github.com/galaxyproject/galaxy/commit/fa2b6baef71984c0559c53ff5750… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Revert "Remove bam to bai converter" This reverts commit 7e2727bc0a74868198e7e457f99df3d1e39f1ddb. Commit: 5f24794efdad757b77c75c3aa111da7a11c5bb47 https://github.com/galaxyproject/galaxy/commit/5f24794efdad757b77c75c3aa111… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add basic .bai datatype Commit: 36706e9eb38728c91c1da2a4cf66ff49f3f44d72 https://github.com/galaxyproject/galaxy/commit/36706e9eb38728c91c1da2a4cf66… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/bam_to_bai.xml Log Message: ----------- Merge pull request #6385 from dannon/revert-baiconverter-removal [18.01] Revert "Remove bam to bai converter" Compare: https://github.com/galaxyproject/galaxy/compare/48fafa8096fd...36706e9eb387 **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/ansible-galaxy] b69cc1: Give an example of starting job handler mules
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/yaml-uwsgi Home: https://github.com/galaxyproject/ansible-galaxy Commit: b69cc10a46132de4dff6172ab112bf2192aad740 https://github.com/galaxyproject/ansible-galaxy/commit/b69cc10a46132de4dff6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M README.md Log Message: ----------- Give an example of starting job handler mules **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/ansible-galaxy] b3a768: Clarify the uWSGI YAML syntax and provide an examp...
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/yaml-uwsgi Home: https://github.com/galaxyproject/ansible-galaxy Commit: b3a7689137fedfc50d101febd9896545125d71cb https://github.com/galaxyproject/ansible-galaxy/commit/b3a7689137fedfc50d10… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M README.md Log Message: ----------- Clarify the uWSGI YAML syntax and provide an example **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/ansible-galaxy] 8417a5: Switch to Ansible 2.4 dynamic task includes to avo...
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/yaml-uwsgi Home: https://github.com/galaxyproject/ansible-galaxy Commit: 8417a5bf92da86c1fd1d8e19dce86c9eaf675701 https://github.com/galaxyproject/ansible-galaxy/commit/8417a5bf92da86c1fd1d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M meta/main.yml M tasks/dependencies.yml M tasks/download.yml M tasks/main.yml Log Message: ----------- Switch to Ansible 2.4 dynamic task includes to avoid tons of skips when running the role in pieces. Commit: 719fa075397f562fb7c14bdb2f71d911c24fa527 https://github.com/galaxyproject/ansible-galaxy/commit/719fa075397f562fb7c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A .gitignore M README.md M defaults/main.yml A filter_plugins/uwsgi_yaml.py M tasks/clone.yml M tasks/errordocs.yml M tasks/static_setup.yml M templates/galaxy.ini.j2 A templates/galaxy.yml.j2 Log Message: ----------- Support for YAML galaxy config Compare: https://github.com/galaxyproject/ansible-galaxy/compare/8417a5bf92da^...719… **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] 533ffa: Add gxy.io redirect for my slides
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 533ffaccc4277ee08ee2db631b8ce1d0cada5dd2 https://github.com/galaxyproject/infrastructure-playbook/commit/533ffaccc42… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M env/galaxy/templates/nginx/gxy.io.j2 Log Message: ----------- Add gxy.io 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] 8a55c4: Add dataselector component
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8a55c4fd5467ed67650f543c4a1955316b569d04 https://github.com/galaxyproject/galaxy/commit/8a55c4fd5467ed67650f543c4a19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: A client/galaxy/scripts/components/DataSelector.vue Log Message: ----------- Add dataselector component Commit: 7cf17001efb8b9491b0e34c8fe063e31d16e1729 https://github.com/galaxyproject/galaxy/commit/7cf17001efb8b9491b0e34c8fe06… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/components/DataSelector.vue Log Message: ----------- Use methods to show and hide dialog Commit: ea5d3d30c4bc356b4d2c1b39e07270e40ff6cb0a https://github.com/galaxyproject/galaxy/commit/ea5d3d30c4bc356b4d2c1b39e072… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Add shared data content access helper Commit: b657fbdd738a0aafb5112445e9aafbb6df9fa3cf https://github.com/galaxyproject/galaxy/commit/b657fbdd738a0aafb5112445e9aa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: A client/galaxy/scripts/components/DataDialog.vue R client/galaxy/scripts/components/DataSelector.vue M client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Remove surrounding div in dialog component Commit: f9e37d43091a61b2102283a57fff858bde8b9f51 https://github.com/galaxyproject/galaxy/commit/f9e37d43091a61b2102283a57fff… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/layout/data.js Log Message: ----------- Append modal to body, display always -- we'll use/destroy() this. Commit: 8a9c6d32321908c6c1bd763cf9cdb91f4c899fc8 https://github.com/galaxyproject/galaxy/commit/8a9c6d32321908c6c1bd763cf9cd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/layout/data.js Log Message: ----------- Add select field to shared data selector Commit: 8a34978decbe8fb70be9eece744aba1b3de03383 https://github.com/galaxyproject/galaxy/commit/8a34978decbe8fb70be9eece744a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Improve error handling, add spinner Commit: 30c42e62d6d724e79177c08ba5c46215a01c9f73 https://github.com/galaxyproject/galaxy/commit/30c42e62d6d724e79177c08ba5c4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Hide second option while loading datasets Commit: 8a858b31bca3c7bd1b1cc7985ac83b89828a2111 https://github.com/galaxyproject/galaxy/commit/8a858b31bca3c7bd1b1cc7985ac8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add default error message, fix alert properties Commit: 6ab1bfbe218689794644d43123dd10021b2ebabe https://github.com/galaxyproject/galaxy/commit/6ab1bfbe218689794644d43123dd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Revise error message handling Commit: 648caa48e49f7a086b20a39fa39cf438f103b9f8 https://github.com/galaxyproject/galaxy/commit/648caa48e49f7a086b20a39fa39c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/layout/data.js Log Message: ----------- Add comments Commit: 59461c2a8f7dbfffa6ed22f54c197a405f992aca https://github.com/galaxyproject/galaxy/commit/59461c2a8f7dbfffa6ed22f54c19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add history dataset id to option text Commit: e662c9754814559232fe0206b2f56548f2fde26c https://github.com/galaxyproject/galaxy/commit/e662c9754814559232fe0206b2f5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Replace select field by table Commit: 1d94c6762e7b830710e5697f99bc2dd6ddeebbb8 https://github.com/galaxyproject/galaxy/commit/1d94c6762e7b830710e5697f99bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add event handlers, close modal Commit: 67c48378c54fc8da0666e88069ce9816c096218e https://github.com/galaxyproject/galaxy/commit/67c48378c54fc8da0666e88069ce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Move search field into modal header Commit: ce76463527a61dc4dba40f4b578645df7693bb81 https://github.com/galaxyproject/galaxy/commit/ce76463527a61dc4dba40f4b5786… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Use default label and file icons Commit: b93e01a784b85d071c3b709de4186278c40a4a4a https://github.com/galaxyproject/galaxy/commit/b93e01a784b85d071c3b709de418… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Use different icons for datasets and collections Commit: d05f72f8e0648fc200e2707fafb9df31724e824c https://github.com/galaxyproject/galaxy/commit/d05f72f8e0648fc200e2707fafb9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/components/DataDialog.vue Log Message: ----------- Add no match notification Commit: cfc63ef24a06266ae9ee55955cce629be7a36558 https://github.com/galaxyproject/galaxy/commit/cfc63ef24a06266ae9ee55955cce… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Remove debug statement Commit: d64bae64580e03a2dd8695a5471f3046323021ff https://github.com/galaxyproject/galaxy/commit/d64bae64580e03a2dd8695a5471f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: A client/galaxy/scripts/components/DataDialog.vue A client/galaxy/scripts/layout/data.js M client/galaxy/scripts/layout/page.js Log Message: ----------- Merge pull request #6195 from guerler/shared_data_selector Common dataset selector Compare: https://github.com/galaxyproject/galaxy/compare/2894dfc8928c...d64bae64580e **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.

1 0

[galaxyproject/galaxy] 996763: Comma-separate tool names in missing tools error m...
by GitHub 22 Jun '18

22 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 9967639bac92eb3f7103794663f41b88f11baa9c https://github.com/galaxyproject/galaxy/commit/9967639bac92eb3f7103794663f4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Comma-separate tool names in missing tools error message Commit: 22d383c39842e0a0198cf2d37ad3832ea1838769 https://github.com/galaxyproject/galaxy/commit/22d383c39842e0a0198cf2d37ad3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-22 (Fri, 22 Jun 2018) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #6378 from guerler/commaseperror [18.05] Comma-separate tool names in missing tools error message Compare: https://github.com/galaxyproject/galaxy/compare/d28ab2a4f31b...22d383c39842 **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.

1 0

[galaxyproject/galaxy] 572f38: move the sanitization to the try/except block
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 572f38d1fb47e914ad10766007c855786e1643a2 https://github.com/galaxyproject/galaxy/commit/572f38d1fb47e914ad10766007c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- move the sanitization to the try/except block as it may fail (and it did, on Main) Commit: d28ab2a4f31b363c236a02a535cc43ab049190ca https://github.com/galaxyproject/galaxy/commit/d28ab2a4f31b363c236a02a535cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6377 from martenson/catch-sanitization-faults [18.05] Catch sanitization faults Compare: https://github.com/galaxyproject/galaxy/compare/6d5be41b3205...d28ab2a4f31b **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.

1 0

[galaxyproject/usegalaxy-playbook] 9b195e: Swarmscale fixes for floating IPs
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9b195e9e8f4edb3a582841082cd5807b4eb23d7d https://github.com/galaxyproject/usegalaxy-playbook/commit/9b195e9e8f4edb3a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: A roles/usegalaxy_swarmscale/files/ansible.cfg M roles/usegalaxy_swarmscale/files/leave.yml M roles/usegalaxy_swarmscale/files/spawn.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- Swarmscale fixes for floating IPs **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.

1 0

[galaxyproject/galaxy] 536c45: Optimizations for dynamic output files collection.
by GitHub 21 Jun '18

21 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 536c45dc1107640a2d0a2e9741f5b6a692ee4173 https://github.com/galaxyproject/galaxy/commit/536c45dc1107640a2d0a2e9741f5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Optimizations for dynamic output files collection. During the set hid and update quota parts of this operation - skip a bunch of extra flushes and skip checking for extra files since these cannot be created in conjunction with dynamic file discovery currently. Cut this part of that operation from about 50 seconds to 7 when creating a collection with 1000 elements on my laptop against a local postgres database. Commit: 2894dfc8928ca1e232b76ae83a84155f7f06e687 https://github.com/galaxyproject/galaxy/commit/2894dfc8928ca1e232b76ae83a84… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-21 (Thu, 21 Jun 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6367 from jmchilton/finish_opt Optimizations for dynamic output file collection. Compare: https://github.com/galaxyproject/galaxy/compare/d1c063d6614f...2894dfc8928c **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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