galaxy-commits May 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] fa577f: For published workflow display, Provide a better e...
by GitHub 04 May '16

04 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa577f75fb77da73b56c2f2c5422aca8e0cc1ea0 https://github.com/galaxyproject/galaxy/commit/fa577f75fb77da73b56c2f2c5422… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- For published workflow display, Provide a better error when the workflow or user cannot be found. Commit: 7a7de38b4ac5df2e2e5cf76ee37497aecc2cbf5e https://github.com/galaxyproject/galaxy/commit/7a7de38b4ac5df2e2e5cf76ee374… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #2302 from dannon/published_workflow_display_404 For published workflow display, Provide a better error when the workf… Compare: https://github.com/galaxyproject/galaxy/compare/2b4fd0f12a41...7a7de38b4ac5

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[galaxyproject/usegalaxy-playbook] a57361: Test was updated
by GitHub 04 May '16

04 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a573617ae3353ccff54489bf3da07c41dcc48f46 https://github.com/galaxyproject/usegalaxy-playbook/commit/a573617ae3353ccf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Test was updated

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[galaxyproject/galaxy] f984b0: Bump sqlite3 version
by GitHub 04 May '16

04 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f984b0d092ac7ff237295d154b66bbfc550b63ee https://github.com/galaxyproject/galaxy/commit/f984b0d092ac7ff237295d154b66… Author: matthdsm <matthias.desmet(a)ugent.be> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Bump sqlite3 version Update sqlite to version 3.1.3 Commit: 2b4fd0f12a412c92ff02bfd56e63d464d6246896 https://github.com/galaxyproject/galaxy/commit/2b4fd0f12a412c92ff02bfd56e63… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/galaxy/web/proxy/js/package.json Log Message: ----------- Merge pull request #2307 from matthdsm/patch-5 Bump sqlite3 version Compare: https://github.com/galaxyproject/galaxy/compare/8d46c5cb2b6b...2b4fd0f12a41

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[galaxyproject/usegalaxy-playbook] bc5a8b: Enable collectl on Test maybe?
by GitHub 04 May '16

04 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bc5a8b7298e390cc4cff32484dff71c56c6c7396 https://github.com/galaxyproject/usegalaxy-playbook/commit/bc5a8b7298e390cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_metrics_conf.xml Log Message: ----------- Enable collectl on Test maybe? Commit: 5eae7eba6f4fc84be90b20104d3f9e19d7a738be https://github.com/galaxyproject/usegalaxy-playbook/commit/5eae7eba6f4fc84b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Update Main masthead message to mention Jetstream Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f7f51aeaf9a3...…

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[galaxyproject/infrastructure-playbook] de4bcf: Update common roles
by GitHub 04 May '16

04 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: de4bcf5d617f394b86af4a16c298344b00d1a09e https://github.com/galaxyproject/infrastructure-playbook/commit/de4bcf5d617… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M common_roles Log Message: ----------- Update common roles

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[galaxyproject/galaxy] ad4c7b: Fix extra blank line for flake8
by GitHub 04 May '16

04 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ad4c7bcb99689d3a73e289801ae6dfe83fc56b6a https://github.com/galaxyproject/galaxy/commit/ad4c7bcb99689d3a73e289801ae6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Fix extra blank line for flake8 Commit: 8d46c5cb2b6b8e6306153f061d6b793432996665 https://github.com/galaxyproject/galaxy/commit/8d46c5cb2b6b8e6306153f061d6b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-04 (Wed, 04 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Merge pull request #2308 from nsoranzo/dev Fix extra blank line for flake8 Compare: https://github.com/galaxyproject/galaxy/compare/d82b5f1ff3c7...8d46c5cb2b6b

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[galaxyproject/galaxy] 55ca1f: Always remove the working directory after creating...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55ca1f5e4e4aa4eff50a1996c76aacd9f80452d8 https://github.com/galaxyproject/galaxy/commit/55ca1f5e4e4aa4eff50a1996c76a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Always remove the working directory after creating the capsule archive. Commit: 0def95f2c846c7115794965fae21d9c49c55e827 https://github.com/galaxyproject/galaxy/commit/0def95f2c846c7115794965fae21… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Use a context manager instead of putting the rmtree in the finally. Commit: a26a931edd066aa8760a8eaa6ad5d4ac2a5e323c https://github.com/galaxyproject/galaxy/commit/a26a931edd066aa8760a8eaa6ad5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Specify the keyword for keyword argument. Commit: 5900c54dbaad159e2777dccf5262962414fb9e6f https://github.com/galaxyproject/galaxy/commit/5900c54dbaad159e2777dccf5262… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Shift context manager Commit: 975a8a4b3b257559b9656e80fcd2a59cbf851b99 https://github.com/galaxyproject/galaxy/commit/975a8a4b3b257559b9656e80fcd2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Remove slightly disruptive space. Commit: a8a1dd278319ed61a8136d18ecfe14ed8319e347 https://github.com/galaxyproject/galaxy/commit/a8a1dd278319ed61a8136d18ecfe… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Merge pull request #4 from dannon/toolshed_capsules Shift context manager Commit: d82b5f1ff3c760ad3380cf1db194c2e020850f93 https://github.com/galaxyproject/galaxy/commit/d82b5f1ff3c760ad3380cf1db194… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/tool_shed/capsule/capsule_manager.py Log Message: ----------- Merge pull request #2294 from davebx/toolshed_capsules Always remove the working directory after creating the capsule archive. Compare: https://github.com/galaxyproject/galaxy/compare/4c00358a1b1d...d82b5f1ff3c7

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[galaxyproject/galaxy] eb15c1: Prepass on remote user header based on maildomain ...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: eb15c147504ca4e871afed5f0ff005552b54e85f https://github.com/galaxyproject/galaxy/commit/eb15c147504ca4e871afed5f0ff0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Prepass on remote user header based on maildomain and normalize config. This resolves an error reported on -dev with maildomain and user being set incorrectly. Commit: ef12ae303577b2cc1967a08b341962f0ef1ffc5a https://github.com/galaxyproject/galaxy/commit/ef12ae303577b2cc1967a08b3419… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako Log Message: ----------- Test fix for christ-h's french language date abbreviations breaking the old library display Commit: 7e93d462392952d27d414ba87d2dd406c9a60be1 https://github.com/galaxyproject/galaxy/commit/7e93d462392952d27d414ba87d2d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Another location where the non-ascii month was breaking display. Commit: 3907d83abe98a77dc6ecfb4abe818ea1bf31e9eb https://github.com/galaxyproject/galaxy/commit/3907d83abe98a77dc6ecfb4abe81… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako Log Message: ----------- Merge pull request #2214 from dannon/old_library_fixes [16.01] Browse library date handling for non-ascii month abbreviations Commit: 912e6ea30ffc8c67033c7815d7adee0cc9db5f90 https://github.com/galaxyproject/galaxy/commit/912e6ea30ffc8c67033c7815d7ad… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- port TS test fix so we can rely on jenkins Commit: 9e980862c8b763cf3dd0209be49f0d2d75a90614 https://github.com/galaxyproject/galaxy/commit/9e980862c8b763cf3dd0209be49f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #2220 from martenson/port-tstestfix [16.01] port TS test fix so we can rely on jenkins Commit: 615b0b444edf6648e174ff950f212c77bb4ed3f5 https://github.com/galaxyproject/galaxy/commit/615b0b444edf6648e174ff950f21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix running workflows in the background when tool bursting is enabled. Commit: cdea922890683f8db0cd9dae3b6eed5695cfd094 https://github.com/galaxyproject/galaxy/commit/cdea922890683f8db0cd9dae3b6e… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2016-05-02 (Mon, 02 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2195 from dannon/remoteuser_work [16.01] Prepass on remote user header based on maildomain and normalize confi… Commit: 063b25f660b6d842c4193469e5c360034562b877 https://github.com/galaxyproject/galaxy/commit/063b25f660b6d842c4193469e5c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #2260 from jmchilton/fix_burst_background_workflows [16.01] Fix running workflows in the background when tool bursting is enabled. Commit: e77d3f009a8e2fb51e97f41b4c47e397c90cbcea https://github.com/galaxyproject/galaxy/commit/e77d3f009a8e2fb51e97f41b4c47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/run.py M templates/webapps/galaxy/library/common/browse_library.mako M templates/webapps/galaxy/library/common/ldda_info.mako M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge branch 'release_16.01' Compare: https://github.com/galaxyproject/galaxy/compare/b79474083b08...e77d3f009a8e

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[galaxyproject/galaxy] 615b0b: Fix running workflows in the background when tool ...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 615b0b444edf6648e174ff950f212c77bb4ed3f5 https://github.com/galaxyproject/galaxy/commit/615b0b444edf6648e174ff950f21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix running workflows in the background when tool bursting is enabled. Commit: 063b25f660b6d842c4193469e5c360034562b877 https://github.com/galaxyproject/galaxy/commit/063b25f660b6d842c4193469e5c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #2260 from jmchilton/fix_burst_background_workflows [16.01] Fix running workflows in the background when tool bursting is enabled. Commit: a54a61897084aa8a74dc5b813e59aaae084157d1 https://github.com/galaxyproject/galaxy/commit/a54a61897084aa8a74dc5b813e59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: 4c00358a1b1d74c71312aa38f58eaff2be3c1e72 https://github.com/galaxyproject/galaxy/commit/4c00358a1b1d74c71312aa38f58e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9fcd759e8dd2...4c00358a1b1d

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[galaxyproject/galaxy] 615b0b: Fix running workflows in the background when tool ...
by GitHub 03 May '16

03 May '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 615b0b444edf6648e174ff950f212c77bb4ed3f5 https://github.com/galaxyproject/galaxy/commit/615b0b444edf6648e174ff950f21… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-27 (Wed, 27 Apr 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix running workflows in the background when tool bursting is enabled. Commit: 063b25f660b6d842c4193469e5c360034562b877 https://github.com/galaxyproject/galaxy/commit/063b25f660b6d842c4193469e5c3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge pull request #2260 from jmchilton/fix_burst_background_workflows [16.01] Fix running workflows in the background when tool bursting is enabled. Commit: a54a61897084aa8a74dc5b813e59aaae084157d1 https://github.com/galaxyproject/galaxy/commit/a54a61897084aa8a74dc5b813e59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-05-03 (Tue, 03 May 2016) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Compare: https://github.com/galaxyproject/galaxy/compare/56bd4ada048a...a54a61897084

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galaxy-commits May 2016