August 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] d24ce8: Add implicit conversions target extension to hda n...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Commit: 66e725b6e33b9e2f1fd447fdec53f025db71e55c https://github.com/galaxyproject/galaxy/commit/66e725b6e33b9e2f1fd447fdec53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 0692f8b4b11df0ea7004e774f2ee3695293a8e6e https://github.com/galaxyproject/galaxy/commit/0692f8b4b11df0ea7004e774f2ee… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/0f5239dd3204...0692f8b4b11d

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[galaxyproject/galaxy] d24ce8: Add implicit conversions target extension to hda n...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Commit: 66e725b6e33b9e2f1fd447fdec53f025db71e55c https://github.com/galaxyproject/galaxy/commit/66e725b6e33b9e2f1fd447fdec53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/4b86f6137f13...66e725b6e33b

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[galaxyproject/galaxy] 33c402: Fix misplaced parenthesis
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 33c4025fabc057a412c2da662b3606afc0726902 https://github.com/galaxyproject/galaxy/commit/33c4025fabc057a412c2da662b36… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Fix misplaced parenthesis Reported by @dpryan79 in https://github.com/galaxyproject/tools-iuc/issues/906#issuecomment-238844304 Commit: f4cb63d6f27f68814bd6131f43c1eee6fa8d099e https://github.com/galaxyproject/galaxy/commit/f4cb63d6f27f68814bd6131f43c1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M tox.ini Log Message: ----------- Pin flake8 version Do not pin when forward-merging to dev branch. Also ignore .tox/ and eggs/ as in #2650 . Commit: 68f718d53bc6bcc44c8ccbe14c79a9fb79c3b9fc https://github.com/galaxyproject/galaxy/commit/68f718d53bc6bcc44c8ccbe14c79… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge pull request #2767 from nsoranzo/release_16.01_handle_complex_repository_dependency_for_package [16.01] Fix misplaced parenthesis Commit: f2f62f340ecd92ebdde51e6d13d5145a6f40cc9e https://github.com/galaxyproject/galaxy/commit/f2f62f340ecd92ebdde51e6d13d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: .ci/flake8_blacklist.txt tox.ini Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Commit: f8cf6f834bd92b82a05250b1c1f0e42957bffb15 https://github.com/galaxyproject/galaxy/commit/f8cf6f834bd92b82a05250b1c1f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M .ci/flake8_blacklist.txt M lib/galaxy/tools/parameters/basic.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M tox.ini Log Message: ----------- Merge branch 'release_16.04' Compare: https://github.com/galaxyproject/galaxy/compare/fb76aa0a938a...f8cf6f834bd9

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[galaxyproject/galaxy] d24ce8: Add implicit conversions target extension to hda n...
by GitHub 12 Aug '16

12 Aug '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: d24ce8b0a49095637d522a3579cf93470fec7a39 https://github.com/galaxyproject/galaxy/commit/d24ce8b0a49095637d522a3579cf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: ceeef39edb5562b1397df19acaf074e8c5412d1b https://github.com/galaxyproject/galaxy/commit/ceeef39edb5562b1397df19acaf0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2779 from nsoranzo/release_16.04_backport_2734 [16.04] Backport #2734 Compare: https://github.com/galaxyproject/galaxy/compare/f2f62f340ecd...ceeef39edb55

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[galaxyproject/infrastructure-playbook] b9ef8f: Add gxsrc user
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: b9ef8f9b0b68955a0b4ded2e69fc8a9f262a6c1e https://github.com/galaxyproject/infrastructure-playbook/commit/b9ef8f9b0b6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M taccenv/group_vars/galaxyservers.yml R taccenv/secret_group_vars/galaxymainservers.yml R taccenv/secret_group_vars/galaxytestservers.yml A taccenv/secret_group_vars/maingalaxyservers.yml A taccenv/secret_group_vars/testgalaxyservers.yml Log Message: ----------- Add gxsrc user

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[galaxyproject/galaxy] c60600: update
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c606003c1000cdbc171c011ccb952c444868271d https://github.com/galaxyproject/galaxy/commit/c606003c1000cdbc171c011ccb95… Author: varunshankar <varunshankar55(a)gmail.com> Date: 2016-07-25 (Mon, 25 Jul 2016) Changed paths: M config/job_conf.xml.sample_advanced A lib/galaxy/jobs/runners/godocker.py Log Message: ----------- update Commit: f68b17c5a805c7208628ec60485150fc7ccd8a88 https://github.com/galaxyproject/galaxy/commit/f68b17c5a805c7208628ec604851… Author: varunshankar <varunshankar55(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Indent Fix Commit: d626c33a131fb3634e4ed3ec2f7130969aca0b0f https://github.com/galaxyproject/galaxy/commit/d626c33a131fb3634e4ed3ec2f71… Author: varunshankar <varunshankar55(a)gmail.com> Date: 2016-07-27 (Wed, 27 Jul 2016) Changed paths: M lib/galaxy/jobs/runners/godocker.py Log Message: ----------- GoDocker runner:Indent fix Commit: 0e79c824800debc4d398ac9b2f6559d09e7c9ac9 https://github.com/galaxyproject/galaxy/commit/0e79c824800debc4d398ac9b2f65… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: A doc/source/dev/Build_a_runner_for_galaxy.md Log Message: ----------- Add tutorial for building a runner for galaxy Commit: a6d3c54522a11d6dc467e737a65b90c47ce5c960 https://github.com/galaxyproject/galaxy/commit/a6d3c54522a11d6dc467e737a65b… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Update job_conf.xml.sample_advanced Commit: 57b2171a79c8993d57256fdbe557fe597fbc9612 https://github.com/galaxyproject/galaxy/commit/57b2171a79c8993d57256fdbe557… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: R lib/galaxy/jobs/runners/godocker.py Log Message: ----------- Delete godocker.py Commit: 5239774fc64e164c0d8ee682d9456149194fbd74 https://github.com/galaxyproject/galaxy/commit/5239774fc64e164c0d8ee682d945… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M doc/source/dev/Build_a_runner_for_galaxy.md Log Message: ----------- Update Build_a_runner_for_galaxy.md Commit: 0b8060619eb1695aa1efd667f45d62fa9a0d87e1 https://github.com/galaxyproject/galaxy/commit/0b8060619eb1695aa1efd667f45d… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-02 (Tue, 02 Aug 2016) Changed paths: M doc/source/dev/Build_a_runner_for_galaxy.md Log Message: ----------- Update Build_a_runner_for_galaxy.md Commit: 54a019435c38d54c1e4f614ff2453907697bbb54 https://github.com/galaxyproject/galaxy/commit/54a019435c38d54c1e4f614ff245… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: R doc/source/dev/Build_a_runner_for_galaxy.md A doc/source/dev/build_a_job_runner.rst Log Message: ----------- Convert to RST, fix image references. Commit: b0eb01cc5bf21f9d7535893b6dd34daae843ef82 https://github.com/galaxyproject/galaxy/commit/b0eb01cc5bf21f9d7535893b6dd3… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: R doc/source/dev/Build_a_runner_for_galaxy.md A doc/source/dev/build_a_job_runner.rst Log Message: ----------- Merge pull request #1 from dannon/doc_dev Convert to RST, fix image references. Commit: 5e639f2bbda3145b925b2565c32e188c7caa55e8 https://github.com/galaxyproject/galaxy/commit/5e639f2bbda3145b925b2565c32e… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: dbd5c848355d12634cf3c9dbb031c29c9a2ea0ec https://github.com/galaxyproject/galaxy/commit/dbd5c848355d12634cf3c9dbb031… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-06 (Sat, 06 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: a06347102dcac5645b92b36c30433051ab6e90ea https://github.com/galaxyproject/galaxy/commit/a06347102dcac5645b92b36c3043… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: 115df2963e339b44c4dec459f19cbc706af2da92 https://github.com/galaxyproject/galaxy/commit/115df2963e339b44c4dec459f19c… Author: Varun Shankar S <varunshankar55(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M doc/source/dev/build_a_job_runner.rst Log Message: ----------- Update build_a_job_runner.rst Commit: 0f5239dd32043eef00269c3ef363c864d83c3dcc https://github.com/galaxyproject/galaxy/commit/0f5239dd32043eef00269c3ef363… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: A doc/source/dev/build_a_job_runner.rst Log Message: ----------- Merge pull request #2700 from varunshankar/doc_dev A tutorial on Build runner for galaxy Compare: https://github.com/galaxyproject/galaxy/compare/8e59a4c84c2c...0f5239dd3204

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[galaxyproject/galaxy] 069d44: Revise repeat block view, remove unecessary table ...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 069d44da36e3067668e99f84d5c756621e0eac66 https://github.com/galaxyproject/galaxy/commit/069d44da36e3067668e99f84d5c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M static/maps/mvc/form/form-repeat.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js Log Message: ----------- Revise repeat block view, remove unecessary table wrapper Commit: 8eabf568330bf7c91bff73d72a648fa4a7a09512 https://github.com/galaxyproject/galaxy/commit/8eabf568330bf7c91bff73d72a64… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Enhance test cases, add repeat block tests Commit: b6e585424ba3ff75659dde1b01e5d624af824e1a https://github.com/galaxyproject/galaxy/commit/b6e585424ba3ff75659dde1b01e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M static/maps/mvc/form/form-repeat.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js Log Message: ----------- Remove unused table library from define/include Commit: 8e59a4c84c2c83806f7162d096d66d68cc39f0c4 https://github.com/galaxyproject/galaxy/commit/8e59a4c84c2c83806f7162d096d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-section.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-section.js M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge pull request #2770 from guerler/revise_repeats Revise repeat block view, remove unecessary table wrapper Compare: https://github.com/galaxyproject/galaxy/compare/f174c8bd4296...8e59a4c84c2c

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[galaxyproject/infrastructure-playbook] 3851a8: Infrastructure for new Galaxy job handler VMs
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3851a8ed924a2fc746938727a1d4f9788aaa6397 https://github.com/galaxyproject/infrastructure-playbook/commit/3851a8ed924… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: A roles/cvmfs/files/cvmfs_wipecache.centos_7 A taccenv/group_vars/slurmclients.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/secret_group_vars/slurmclients.yml A taccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Infrastructure for new Galaxy job handler VMs

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[galaxyproject/galaxy] 87d623: Improve startup scripts
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87d6239c362397824f6d145b56d564dfb3d4b774 https://github.com/galaxyproject/galaxy/commit/87d6239c362397824f6d145b56d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Improve startup scripts Fix errors reported by shellcheck Commit: f174c8bd4296a7fa74d23af39cb8d0523a69aa4f https://github.com/galaxyproject/galaxy/commit/f174c8bd4296a7fa74d23af39cb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #2765 from nsoranzo/run_sh Improve startup scripts Compare: https://github.com/galaxyproject/galaxy/compare/ac5ce47888e0...f174c8bd4296

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[galaxyproject/infrastructure-playbook] d8dec9: Allow jenkins on slaves to log in to the starforge...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d8dec916e7b50acf2973e1f5081eac8e305758cf https://github.com/galaxyproject/infrastructure-playbook/commit/d8dec916e7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Allow jenkins on slaves to log in to the starforge builder

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