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

[galaxyproject/galaxy] b908ea: Fix collection mapping to allow mapping over multi...
by GitHub 05 Jun '18

05 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b908ea4530a44993efb8682281d13ebc87cc339b https://github.com/galaxyproject/galaxy/commit/b908ea4530a44993efb8682281d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Fix collection mapping to allow mapping over multi-data inputs. It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work. Commit: 8f5552f50cda2f5b91bc6fdbfe925726ed6e6077 https://github.com/galaxyproject/galaxy/commit/8f5552f50cda2f5b91bc6fdbfe92… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix up subcollection_type Commit: 0ba8090d22c6f7e8b9aff863bb6d37723db46492 https://github.com/galaxyproject/galaxy/commit/0ba8090d22c6f7e8b9aff863bb6d… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Merge pull request #6255 from jmchilton/subcollection_mapping_with_multi_data_inputs Fix collection mapping to allow subcollection mapping over multi-data inputs. Compare: https://github.com/galaxyproject/galaxy/compare/6911153c307b...0ba8090d22c6 **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] 3d9593: Test mutable configs
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3d95937091259eee7cae0e96bda31cae0f52b6aa https://github.com/galaxyproject/usegalaxy-playbook/commit/3d95937091259eee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.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: ----------- Test mutable configs **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] ad02eb: Web workers need the path to dynamic job modules n...
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ad02eb60229d95f485209e2c090592bb78330f16 https://github.com/galaxyproject/usegalaxy-playbook/commit/ad02eb60229d95f4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/common/templates/supervisor/galaxy.j2 Log Message: ----------- Web workers need the path to dynamic job modules now due to galaxyproject/galaxy#6215. Commit: 8ea5e20529cd490921e7026edcc44e4f6c3e4e6d https://github.com/galaxyproject/usegalaxy-playbook/commit/8ea5e20529cd4909… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/common/templates/supervisor/galaxy.j2 Log Message: ----------- Fix typo Commit: 3fc291878724b0bf5ea4191a8f2ab7c4079dfaa3 https://github.com/galaxyproject/usegalaxy-playbook/commit/3fc291878724b0bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/main/files/galaxy/config/pulsar_bridges_actions.yml M env/test/files/galaxy/config/pulsar_bridges_actions.yml Log Message: ----------- Move data from pylon2 to pylon5 on Bridges Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c3db7e37bbcc...… **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] c3db7e: Updated fastQC to 0.72, DiffBind to 2.6.6.3, insta...
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3db7e37bbcc6b248b4c4cc5a9b946789d049ce1 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3db7e37bbcc6b24… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 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: ----------- Updated fastQC to 0.72, DiffBind to 2.6.6.3, installed BCFTools call **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] 132071: Increase TLS session/renegotiate values for ProFTP...
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 132071450beb74f53a918d2c9dd090aa9c9d659b https://github.com/galaxyproject/usegalaxy-playbook/commit/132071450beb74f5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) 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/templates/tls.conf.j2 Log Message: ----------- Increase TLS session/renegotiate values for ProFTPD on both Test and Main **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] 47c654: Main mutable configs
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 47c6548ee7e26fcb698b812e971be21c0875bea8 https://github.com/galaxyproject/usegalaxy-playbook/commit/47c6548ee7e26fcb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 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: ----------- Main mutable configs **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] f110b6: Update Test
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f110b6355efcbe245c6ae791a220f3b5bc4e2382 https://github.com/galaxyproject/usegalaxy-playbook/commit/f110b6355efcbe24… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test **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] 390278: run star_fusion on bridges
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3902785a66bfe8da46e36224e6c1eb39922d2805 https://github.com/galaxyproject/usegalaxy-playbook/commit/3902785a66bfe8da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-23 (Fri, 23 Mar 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- run star_fusion on bridges should have similar mem reqs as rna_star Commit: e12bdd990e49ce8243a0c27f67ef7fcca754d190 https://github.com/galaxyproject/usegalaxy-playbook/commit/e12bdd990e49ce82… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Merge pull request #107 from galaxyproject/martenson-patch-1 run star_fusion on bridges Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3ec46d06eb5b...… **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] 671c4d: fix link to workflow list
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/fix_workflow_link Home: https://github.com/galaxyproject/galaxy Commit: 671c4d4f5fad7d15e6b9f70d595cf9f14ec6aeda https://github.com/galaxyproject/galaxy/commit/671c4d4f5fad7d15e6b9f70d595c… Author: Björn Grüning <bjoern.gruening(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- fix link to workflow list **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] 38dc3b: Test element_identifier usage with single data par...
by GitHub 04 Jun '18

04 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38dc3baef128e8d5b45a329552e976fe8a6fab49 https://github.com/galaxyproject/galaxy/commit/38dc3baef128e8d5b45a329552e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-24 (Thu, 24 May 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_single_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test element_identifier usage with single data parameters, in repeat/cond. Commit: 6ace37e910f041442f8b45b76c143fd0dab5ca8d https://github.com/galaxyproject/galaxy/commit/6ace37e910f041442f8b45b76c14… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M test/functional/tools/identifier_single_in_repeat.xml Log Message: ----------- Use 4-space indent in identifier_single_in_repeat test tool Commit: 48fda8debca521a8803513ba8b19ebd92fdec904 https://github.com/galaxyproject/galaxy/commit/48fda8debca521a8803513ba8b19… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M test/functional/tools/identifier_single_in_repeat.xml Log Message: ----------- Merge pull request #68 from mvdbeek/one_more_identifier_test Use 4-space indent in identifier_single_in_repeat test tool Commit: 6911153c307ba25525df7c165b4f10b4260964ac https://github.com/galaxyproject/galaxy/commit/6911153c307ba25525df7c165b4f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/identifier_single_in_repeat.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6213 from jmchilton/one_more_identifier_test Test element_identifier usage with single data parameters, in repeat/cond. Compare: https://github.com/galaxyproject/galaxy/compare/b08455ecab5f...6911153c307b **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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