galaxy-commits February 2019

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[galaxyproject/infrastructure-playbook] 76496a: Set up Mailman volume on claven
by Nate Coraor 28 Feb '19

28 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 76496a8ee536cbb4196e896d063fb40e5b21eaad https://github.com/galaxyproject/infrastructure-playbook/commit/76496a8ee53… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: A env/mailman/host_vars/claven.galaxyproject.org.yml Log Message: ----------- Set up Mailman volume on claven Commit: 7fc8b8fb64036130970911a6a09541a68089903f https://github.com/galaxyproject/infrastructure-playbook/commit/7fc8b8fb640… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M env/mailman/TODO.txt A env/mailman/_inc_pgdata.yml M env/mailman/group_vars/listservers/vars.yml M env/mailman/listservers.yml Log Message: ----------- Move claven's $PGDATA to Mailman's EBS volume Commit: 0bfa509e0fbfc38d3d7ef4dd47ede1a074c2e79d https://github.com/galaxyproject/infrastructure-playbook/commit/0bfa509e0fb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M env/mailman/group_vars/listservers/vars.yml M requirements.yml Log Message: ----------- Small Mailman fixes and updates Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/5f00380ffa…

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[galaxyproject/galaxy] c1fd5d: Open TS workflow with UTF-8 encoding
by Martin Cech 28 Feb '19

28 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1fd5dc99245bdce966923da02c5820277c78fbd https://github.com/galaxyproject/galaxy/commit/c1fd5dc99245bdce966923da02c5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Open TS workflow with UTF-8 encoding Commit: 3ee40dfb08c40f5f2f1cb783510da6dc86dd7d35 https://github.com/galaxyproject/galaxy/commit/3ee40dfb08c40f5f2f1cb783510d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Drop redundant install keyword Already handled in 51d167b85d218c3181ebd6f6f67c7333f981746a Commit: 34cb25ba74116a97626b26c26f3bc7d3889f47b8 https://github.com/galaxyproject/galaxy/commit/34cb25ba74116a97626b26c26f3b… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Use more specific exception Co-Authored-By: mvdbeek <m.vandenbeek(a)gmail.com> Commit: ebec090e46c19bec9ad036d793011db2e0143eeb https://github.com/galaxyproject/galaxy/commit/ebec090e46c19bec9ad036d79301… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge pull request #7423 from mvdbeek/minor_fixes Drop unused install keyword and load TS workflows with utf-8 encoding Compare: https://github.com/galaxyproject/galaxy/compare/bb9cfc610cf1...ebec090e46c1

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[galaxyproject/galaxy] 9e0d3b: Fix workflow loading on systems with ASCII locale
by Martin Cech 28 Feb '19

28 Feb '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9e0d3b69cabe73a7b839e62723e73d52c2c41c69 https://github.com/galaxyproject/galaxy/commit/9e0d3b69cabe73a7b839e62723e7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Fix workflow loading on systems with ASCII locale Fixes https://github.com/galaxyproject/galaxy/issues/7421, though it's very likely Galaxy won't play well when python is falling back to ASCII as default encoding. WorkflowStep.label is backed by a 255 character unicode string, but tool_inputs is JSONType, which might have integer or float values (in principle), so we play it safe by casting to unicode. Commit: 13c175a8096b3d17b4002906cf8e13ab01865222 https://github.com/galaxyproject/galaxy/commit/13c175a8096b3d17b4002906cf8e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #7422 from mvdbeek/fix_workflow_loading [18.09] Fix workflow loading on systems with ASCII locale Compare: https://github.com/galaxyproject/galaxy/compare/9b72f5a880e3...13c175a8096b

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[galaxyproject/galaxy] 51d167: Fix dependency installation in UI
by Nicola Soranzo 28 Feb '19

28 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51d167b85d218c3181ebd6f6f67c7333f981746a https://github.com/galaxyproject/galaxy/commit/51d167b85d218c3181ebd6f6f67c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Fix dependency installation in UI We need to pass the install kwarg here. Broken in https://github.com/galaxyproject/galaxy/commit/2d3ab4ce1205aec24664225d74b2… Commit: 4dae35ea67be33cf4e9739433d3c4cec4f1ff46e https://github.com/galaxyproject/galaxy/commit/4dae35ea67be33cf4e9739433d3c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Merge pull request #7418 from mvdbeek/fix_install_through_managment_ui [19.01] Fix dependency installation in UI Commit: bb9cfc610cf12a2ac1df035bc381649dc4636553 https://github.com/galaxyproject/galaxy/commit/bb9cfc610cf12a2ac1df035bc381… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/tools/deps/views.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0a39badc7981...bb9cfc610cf1

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[galaxyproject/infrastructure-playbook] 5f0038: update TODO
by Nate Coraor 28 Feb '19

28 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5f00380ffae1198135c590bf0a9a6cb4143758c6 https://github.com/galaxyproject/infrastructure-playbook/commit/5f00380ffae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M env/mailman/TODO.txt Log Message: ----------- update TODO

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[galaxyproject/infrastructure-playbook] c7f68e: Fix mailman https redirect
by Nate Coraor 28 Feb '19

28 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c7f68e3c3ae1d09ab617441f384f74763f5e70e5 https://github.com/galaxyproject/infrastructure-playbook/commit/c7f68e3c3ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/mailman/templates/nginx/mailman.j2 Log Message: ----------- Fix mailman https redirect

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[galaxyproject/infrastructure-playbook] 525fe5: Update TODO again
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 525fe50efdf127853407b2249804cf6626c481e1 https://github.com/galaxyproject/infrastructure-playbook/commit/525fe50efdf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/mailman/TODO.txt Log Message: ----------- Update TODO again

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[galaxyproject/infrastructure-playbook] 8eacd8: Update common_roles
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8eacd8e2361ebb45d2780233aab01147fa487d85 https://github.com/galaxyproject/infrastructure-playbook/commit/8eacd8e2361… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M common_roles Log Message: ----------- Update common_roles Commit: 798d37cf566e7a09e4896a2e7cbd047592eeef0b https://github.com/galaxyproject/infrastructure-playbook/commit/798d37cf566… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/mailman/TODO.txt Log Message: ----------- Update TODO Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/0f9484e5ec…

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[galaxyproject/usegalaxy-playbook] deff27: Test/Main mutable configs
by Nate Coraor 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: deff27b4c5e3b091ed13400ddde44011dfd6531c https://github.com/galaxyproject/usegalaxy-playbook/commit/deff27b4c5e3b091… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Test/Main mutable configs

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[galaxyproject/usegalaxy-playbook] 03a24a: Installed column_maker 1.2.0 on main.
by Dave B. 27 Feb '19

27 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 03a24a03f68e933ad299a50b1b8740a509cca8d5 https://github.com/galaxyproject/usegalaxy-playbook/commit/03a24a03f68e933a… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed column_maker 1.2.0 on main. Commit: f13ae825c44cb52f898efb92a205fb5e62ea3944 https://github.com/galaxyproject/usegalaxy-playbook/commit/f13ae825c44cb52f… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-27 (Wed, 27 Feb 2019) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/be2c2cebf741...…

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galaxy-commits February 2019