galaxy-commits March 2016

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[galaxyproject/usegalaxy-playbook] 2eaf31: Add labels and move gemini.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2eaf317b3885999221b39b606004ae92478f5096 https://github.com/galaxyproject/usegalaxy-playbook/commit/2eaf317b38859992… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- Add labels and move gemini. Commit: 73c7f2e96577d664e299bf1cefbbca88581302a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/73c7f2e96577d664… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- Merge pull request #18 from davebx/clean_gemini Add labels and move gemini. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e9dcdbb7df55...…

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[galaxyproject/usegalaxy-playbook] 7833ec: remove slide from Main and update submodule
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7833ec74dba026b003fad88e716f5bda087a8ed6 https://github.com/galaxyproject/usegalaxy-playbook/commit/7833ec74dba026b0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- remove slide from Main and update submodule Commit: e9dcdbb7df55aed387db294612c82e4e95f14e6e https://github.com/galaxyproject/usegalaxy-playbook/commit/e9dcdbb7df55aed3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M stage/group_vars/all.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/9ad17375108f...…

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[galaxyproject/galaxy] 3a1c84: Remove duplicate help target
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3a1c84690239fd7a23393f0ba2e714ab8c659557 https://github.com/galaxyproject/galaxy/commit/3a1c84690239fd7a23393f0ba2e7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Remove duplicate help target And reformat for using existing help-text helper Fixes #1979 Commit: 9a6d3962307f345da34f338f42eebf570562cd63 https://github.com/galaxyproject/galaxy/commit/9a6d3962307f345da34f338f42ee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Fix docs Makefile target. Commit: 9d8957d121108549c1448a959aaf1061091a0bec https://github.com/galaxyproject/galaxy/commit/9d8957d121108549c1448a959aaf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Document a couple other targets Commit: be78aac509bc3a84743b418544702bfca6b50eda https://github.com/galaxyproject/galaxy/commit/be78aac509bc3a84743b41854470… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #1980 from erasche/fix-1979 Remove duplicate help target Compare: https://github.com/galaxyproject/galaxy/compare/0dc57b08e851...be78aac509bc

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[galaxyproject/galaxy] 133f77: Fix 'Resend verification' link in inactive user me...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 133f77413e9fb933ec1964d279408c1fb8846db4 https://github.com/galaxyproject/galaxy/commit/133f77413e9fb933ec1964d27940… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- Fix 'Resend verification' link in inactive user message box which would display as [Object object] Commit: fef166545c36df5c7ba73924c7b0ea4e1d44ec82 https://github.com/galaxyproject/galaxy/commit/fef166545c36df5c7ba73924c7b0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Layout: Fix optional panel rendering and associated inline css Commit: dd476fc42c57b5e17d8e1e342d7a597b986b6b3e https://github.com/galaxyproject/galaxy/commit/dd476fc42c57b5e17d8e1e342d7a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- Merge pull request #1978 from carlfeberhard/release_16.01 [16.01] Fixes to page.js Compare: https://github.com/galaxyproject/galaxy/compare/fa1414759e60...dd476fc42c57

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[galaxyproject/galaxy] 975937: Fix docker tool execution for #1688.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 975937ec9d18287fe89a7ee9eda0952e22284ac7 https://github.com/galaxyproject/galaxy/commit/975937ec9d18287fe89a7ee9eda0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Fix docker tool execution for #1688. Thanks for @kellrott for the bug report. \#minor Commit: 0dc57b08e851544cfd1f9e4cd94de9971db2b24d https://github.com/galaxyproject/galaxy/commit/0dc57b08e851544cfd1f9e4cd94d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1974 from jmchilton/docker_fix Fix docker tool execution for #1688. Compare: https://github.com/galaxyproject/galaxy/compare/67b7294a7278...0dc57b08e851

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Compare: https://github.com/galaxyproject/galaxy/compare/9cff686d6d94...a2114fdd0e23

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[galaxyproject/usegalaxy-playbook] 9ad173: Increase BMW-MEM indexer to 16GB of memory and run...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9ad17375108fc081cc6f063c8d768a69ec56295c https://github.com/galaxyproject/usegalaxy-playbook/commit/9ad17375108fc081… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Increase BMW-MEM indexer to 16GB of memory and run it with the datamanager server as its handler.

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[galaxyproject/galaxy] eee044: Work toward automating deployment.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eee044aa707f9fa6d4c800b4d655fd01b2e08e84 https://github.com/galaxyproject/galaxy/commit/eee044aa707f9fa6d4c800b4d655… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M Makefile M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Work toward automating deployment. Create new makefile targets for release management. - ``release-create-issue``: Automates creating a release checklist - https://github.com/jmchilton/galaxy/issues/41) Check list contains actual tailored ``make`` commands and links (for PRs and issues). - ``release-check-metadata``: Checks milestone PRs for required metadata needed for generating bootstrapped release notes. ` ``release-bootstrap-history``: Bootstrap release notes from PRs and metadata. - ``release-check-blocking-prs``: Check for PRs blocking release, should happen before branching release and before tagging release. - ``release-check-blocking-issues``: Check for Issues blocking release, should happen before tagging release. (Only allowed issue is the release creation issue.) The issue created with ``release-create-issue`` documents how and when to execute subsequent ``make`` targets (including the target to create the issue for the next release). This PR contains a bunch of other enhancements to the bootstrap_history.py script to enable these targets and renames ``create_release_rc`` Makefile target so all release related targets start with the prefix ``release-``. Conflicts: Makefile Commit: 67b7294a7278f262f0e2238b0094cef5fc835771 https://github.com/galaxyproject/galaxy/commit/67b7294a7278f262f0e2238b0094… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #1613 from jmchilton/release_process Work toward automating release management. Compare: https://github.com/galaxyproject/galaxy/compare/4bf8adbb6462...67b7294a7278

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[galaxyproject/galaxy] 583461: Fix dom duplication
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58346169dfbe89f845a3f2317bde514c3e65f79f https://github.com/galaxyproject/galaxy/commit/58346169dfbe89f845a3f2317bde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix dom duplication Commit: fa1414759e604073bc45fe3f2b15dc9f21c72c4c https://github.com/galaxyproject/galaxy/commit/fa1414759e604073bc45fe3f2b15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1976 from guerler/fix_ui_000 [16.01] Fix dom duplication Commit: 4bf8adbb6462456a201a6f69862e0d3fdb1da222 https://github.com/galaxyproject/galaxy/commit/4bf8adbb6462456a201a6f69862e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/45c17318889d...4bf8adbb6462

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[galaxyproject/galaxy] 583461: Fix dom duplication
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 58346169dfbe89f845a3f2317bde514c3e65f79f https://github.com/galaxyproject/galaxy/commit/58346169dfbe89f845a3f2317bde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix dom duplication Commit: fa1414759e604073bc45fe3f2b15dc9f21c72c4c https://github.com/galaxyproject/galaxy/commit/fa1414759e604073bc45fe3f2b15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1976 from guerler/fix_ui_000 [16.01] Fix dom duplication Compare: https://github.com/galaxyproject/galaxy/compare/30750c32e481...fa1414759e60

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galaxy-commits March 2016