- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e8f5a1: Fix LocalShellRunner
by John Chilton 01 Mar '19

01 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: e8f5a13f3b4d0f57819db18bb6cde086b92eb6c8 https://github.com/galaxyproject/galaxy/commit/e8f5a13f3b4d0f57819db18bb6cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Fix LocalShellRunner All the `cmd` coming from the plugins are strings, so if cmd is a string we use `shell=True`, brings this on par with the Remote Shell plugins (which consume strings). Should fix https://github.com/galaxyproject/galaxy/issues/7269. Commit: a12d9e367cae5eb19eec905385d6cb9e5ad0826c https://github.com/galaxyproject/galaxy/commit/a12d9e367cae5eb19eec905385d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Merge pull request #7438 from mvdbeek/fix_shell_runner [18.09] Fix LocalShellRunner Compare: https://github.com/galaxyproject/galaxy/compare/68e3568bb259...a12d9e367cae

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[galaxyproject/galaxy] 47af06: Add tool hover
by Martin Cech 01 Mar '19

01 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47af069a34d21a034de6250676663884305c371b https://github.com/galaxyproject/galaxy/commit/47af069a34d21a034de625067666… Author: Helena Rasche <hxr(a)hx42.org> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Add tool hover Commit: 480dddac31f4ef7d583ba2ef50d7e13c6e1c12ce https://github.com/galaxyproject/galaxy/commit/480dddac31f4ef7d583ba2ef50d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7437 from erasche/tool-hover Add tool hover Compare: https://github.com/galaxyproject/galaxy/compare/4a63ad753e6e...480dddac31f4

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[galaxyproject/usegalaxy-playbook] 692146: Installed bowtie1 wrapper version 1.2.0 on test.
by Dave B. 01 Mar '19

01 Mar '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 69214646d6cee31af02d4aac562d03904e5f17c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/69214646d6cee31a… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-03-01 (Fri, 01 Mar 2019) 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: ----------- Installed bowtie1 wrapper version 1.2.0 on test.

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[galaxyproject/galaxy] 203937: send post data in payload per @mvdbeek suggestion
by Nicola Soranzo 01 Mar '19

01 Mar '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2039376ddf21abb8e56b4ec984ea9d7fed46efb8 https://github.com/galaxyproject/galaxy/commit/2039376ddf21abb8e56b4ec984ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- send post data in payload per @mvdbeek suggestion Commit: c40689dbd5fe27cace5c11a50d806445aefae97a https://github.com/galaxyproject/galaxy/commit/c40689dbd5fe27cace5c11a50d80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #7432 from martenson/fix-lib-paths [19.01] send post data in payload Commit: 4a63ad753e6e502ebb89643f675f5d25d260251b https://github.com/galaxyproject/galaxy/commit/4a63ad753e6e502ebb89643f675f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c671b5372789...4a63ad753e6e

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[galaxyproject/galaxy] 203937: send post data in payload per @mvdbeek suggestion
by Marius van den Beek 01 Mar '19

01 Mar '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 2039376ddf21abb8e56b4ec984ea9d7fed46efb8 https://github.com/galaxyproject/galaxy/commit/2039376ddf21abb8e56b4ec984ea… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- send post data in payload per @mvdbeek suggestion Commit: c40689dbd5fe27cace5c11a50d806445aefae97a https://github.com/galaxyproject/galaxy/commit/c40689dbd5fe27cace5c11a50d80… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #7432 from martenson/fix-lib-paths [19.01] send post data in payload Compare: https://github.com/galaxyproject/galaxy/compare/64a0152a6b82...c40689dbd5fe

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[galaxyproject/galaxy] 9e0d3b: Fix workflow loading on systems with ASCII locale
by Nicola Soranzo 01 Mar '19

01 Mar '19

Branch: refs/heads/dev 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 Commit: 9a26de1b4b5a96eacab97aca2e74b994f38bdc31 https://github.com/galaxyproject/galaxy/commit/9a26de1b4b5a96eacab97aca2e74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch another Slurm memory cgroup creation error message Commit: 68e3568bb25928a86283e3d50411d64acd523c52 https://github.com/galaxyproject/galaxy/commit/68e3568bb25928a86283e3d50411… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #7429 from natefoo/slurm-cgroup-message-fix [18.09] Catch another Slurm memory cgroup creation error message Commit: 64a0152a6b82dd28c7fb5cb6a784e7eced988906 https://github.com/galaxyproject/galaxy/commit/64a0152a6b82dd28c7fb5cb6a784… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/workflows.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Commit: c671b53727896c199227e33bed67d5a00c05cfd7 https://github.com/galaxyproject/galaxy/commit/c671b53727896c199227e33bed67… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/workflows.py Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ebec090e46c1...c671b5372789

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[galaxyproject/galaxy] 9e0d3b: Fix workflow loading on systems with ASCII locale
by Nicola Soranzo 01 Mar '19

01 Mar '19

Branch: refs/heads/release_19.01 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 Commit: 9a26de1b4b5a96eacab97aca2e74b994f38bdc31 https://github.com/galaxyproject/galaxy/commit/9a26de1b4b5a96eacab97aca2e74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch another Slurm memory cgroup creation error message Commit: 68e3568bb25928a86283e3d50411d64acd523c52 https://github.com/galaxyproject/galaxy/commit/68e3568bb25928a86283e3d50411… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #7429 from natefoo/slurm-cgroup-message-fix [18.09] Catch another Slurm memory cgroup creation error message Commit: 64a0152a6b82dd28c7fb5cb6a784e7eced988906 https://github.com/galaxyproject/galaxy/commit/64a0152a6b82dd28c7fb5cb6a784… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py M lib/galaxy/managers/workflows.py Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/4dae35ea67be...64a0152a6b82

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[galaxyproject/galaxy] 9a26de: Catch another Slurm memory cgroup creation error m...
by Nicola Soranzo 01 Mar '19

01 Mar '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 9a26de1b4b5a96eacab97aca2e74b994f38bdc31 https://github.com/galaxyproject/galaxy/commit/9a26de1b4b5a96eacab97aca2e74… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-28 (Thu, 28 Feb 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Catch another Slurm memory cgroup creation error message Commit: 68e3568bb25928a86283e3d50411d64acd523c52 https://github.com/galaxyproject/galaxy/commit/68e3568bb25928a86283e3d50411… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-03-01 (Fri, 01 Mar 2019) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #7429 from natefoo/slurm-cgroup-message-fix [18.09] Catch another Slurm memory cgroup creation error message Compare: https://github.com/galaxyproject/galaxy/compare/13c175a8096b...68e3568bb259

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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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