January 2019 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 35fe3b: Not all workflow outputs have a UUID
by GitHub 24 Jan '19

24 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 35fe3bf716e4f527755f75ebb99b9dbdb777e37d https://github.com/galaxyproject/galaxy/commit/35fe3bf716e4f527755f75ebb99b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Not all workflow outputs have a UUID Commit: f2a454c776bea547967c867e47a827a9a969f67c https://github.com/galaxyproject/galaxy/commit/f2a454c776bea547967c867e47a8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix output uuid comparison Commit: 1a4c1ec514024bb5ee71997afe54158083ca5222 https://github.com/galaxyproject/galaxy/commit/1a4c1ec514024bb5ee71997afe54… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-01-24 (Thu, 24 Jan 2019) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #7258 from mvdbeek/fix_workflow_uuid_access [18.09] Not all workflow outputs have a UUID Compare: https://github.com/galaxyproject/galaxy/compare/920f07369dc5...1a4c1ec51402 **NOTE:** GitHub Services has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ We will provide an alternative path for the email notifications by January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 703c07: Update .loc paths for gemini.
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 703c07670970ff2c473e7c6fcf4b36d032ad1f0f https://github.com/galaxyproject/usegalaxy-playbook/commit/703c07670970ff2c… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update .loc paths for gemini. **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] 1e558f: Update ProFTPD role
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1e558f777516658157f489347a2227dfe500f439 https://github.com/galaxyproject/usegalaxy-playbook/commit/1e558f7775166581… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M env/main/group_vars/ftpservers/vars.yml M env/test/group_vars/ftpservers/vars.yml M roles/galaxyproject.proftpd/README.md M roles/galaxyproject.proftpd/defaults/main.yml M roles/galaxyproject.proftpd/meta/.galaxy_install_info M roles/galaxyproject.proftpd/tasks/tls.yml Log Message: ----------- Update ProFTPD role **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] 7fa74f: Update gemini wrappers and binary to version 0.20....
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7fa74f8832275444e1d88582765026c8d986dea8 https://github.com/galaxyproject/usegalaxy-playbook/commit/7fa74f8832275444… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update gemini wrappers and binary to version 0.20.1 **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/ansible-galaxy] 7f6bf0: make it a list
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 7f6bf00101efb5f5b48a20e894988b2664c1059f https://github.com/galaxyproject/ansible-galaxy/commit/7f6bf00101efb5f5b48a… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M README.md Log Message: ----------- make it a 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/ansible-galaxy] 008f65: fix condition again
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 008f65ba431ddf7d3c7526727e7d7bcdd8278ab3 https://github.com/galaxyproject/ansible-galaxy/commit/008f65ba431ddf7d3c75… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M tasks/main.yml Log Message: ----------- fix condition again **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/ansible-galaxy] 44b6d2: fix condition
by GitHub 23 Jan '19

23 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 44b6d2e5daac3637e99cf234f38a0e8224ca4f0b https://github.com/galaxyproject/ansible-galaxy/commit/44b6d2e5daac3637e99c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-23 (Wed, 23 Jan 2019) Changed paths: M tasks/main.yml Log Message: ----------- fix condition **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] be7628: Remove unneeded conditional requirements
by GitHub 22 Jan '19

22 Jan '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: be7628531927ca826e1b0d05f435da19e721ea8d https://github.com/galaxyproject/galaxy/commit/be7628531927ca826e1b0d05f435… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Remove unneeded conditional requirements They are already included in `requirements.txt` . `ConditionalDependencies.check_python_openid()` was already removed in commit f31d61b71c739c03e5068bff188a56f175a18297 . Commit: d0373c6a956cea15618db2021f3501117078a23f https://github.com/galaxyproject/galaxy/commit/d0373c6a956cea15618db2021f35… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst Log Message: ----------- ``make config-rebuild`` Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 . Commit: d5b306dd216e1b8d0f2ed34c52e562df643c8069 https://github.com/galaxyproject/galaxy/commit/d5b306dd216e1b8d0f2ed34c52e5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-01-21 (Mon, 21 Jan 2019) Changed paths: M doc/source/admin/authentication.md M doc/source/admin/config.rst R doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.web.framework.rst Log Message: ----------- Remove OpenID auth from docs Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 . Commit: 599f5d5a334627451e78cf7349aec55035fcb8f9 https://github.com/galaxyproject/galaxy/commit/599f5d5a334627451e78cf7349ae… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M config/galaxy.yml.sample M config/tool_shed.yml.sample M doc/source/admin/authentication.md M doc/source/admin/config.rst M doc/source/admin/galaxy_options.rst R doc/source/lib/galaxy.openid.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.web.framework.rst M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #7247 from nsoranzo/unneeded_conditional_reqs Remove unneeded conditional requirements Compare: https://github.com/galaxyproject/galaxy/compare/c58f9acf7fe2...599f5d5a3346 **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] 31c71f: strip() text when loading xml
by GitHub 22 Jan '19

22 Jan '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 31c71fbd6fb65cc4a4358e8b415d48885e73e7de https://github.com/galaxyproject/galaxy/commit/31c71fbd6fb65cc4a4358e8b415d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- strip() text when loading xml Should fix https://github.com/galaxyproject/galaxy/issues/7250. Commit: 920f07369dc553a31a848fe044b563b83bd0f2dc https://github.com/galaxyproject/galaxy/commit/920f07369dc553a31a848fe044b5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: M lib/galaxy/util/__init__.py M test/unit/test_utils.py Log Message: ----------- Merge pull request #7252 from mvdbeek/fix_shed_tool_conf_parsing [18.09] strip() text when parsing xml Compare: https://github.com/galaxyproject/galaxy/compare/889c1026c089...920f07369dc5 **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/ansible-galaxy] 4d873f: add common startup task
by GitHub 22 Jan '19

22 Jan '19

Branch: refs/heads/eu Home: https://github.com/galaxyproject/ansible-galaxy Commit: 4d873f72e958d9768244933c075ecf0c8ef4abc1 https://github.com/galaxyproject/ansible-galaxy/commit/4d873f72e958d9768244… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-01-22 (Tue, 22 Jan 2019) Changed paths: A tasks/build_client.yml M tasks/main.yml Log Message: ----------- add common startup task **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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