galaxy-commits April 2016

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] 912e6e: port TS test fix so we can rely on jenkins
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/3907d83abe98...9e980862c8b7

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[galaxyproject/infrastructure-playbook] 482643: Additional TACC JS nodes
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 482643cabff22b5cff626a499b6cacb20963e8d8 https://github.com/galaxyproject/infrastructure-playbook/commit/482643cabff… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Additional TACC JS nodes

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[galaxyproject/galaxy] 9681de: Improve handling of a missing R environment.
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9681ded30b087904005774435b2acc201a618a0a https://github.com/galaxyproject/galaxy/commit/9681ded30b087904005774435b2a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Improve handling of a missing R environment. Previously, the error message 'Missing R environment. Please check your specified R installation exists.' would be displayed in an obscure location in the log. With this change, galaxy will set the tool dependency to Error and display the error message in the admin panel. Commit: d0028bde0fee5a6158473a56ad357e942a92b7cb https://github.com/galaxyproject/galaxy/commit/d0028bde0fee5a6158473a56ad35… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #2215 from davebx/td_fix Improve handling of a missing R environment. Compare: https://github.com/galaxyproject/galaxy/compare/c563d37bfd8d...d0028bde0fee

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[galaxyproject/infrastructure-playbook] d4f94a: Jetstream GO!
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d4f94ab28a7c4dac8a11ac06b3b44530baf52f3f https://github.com/galaxyproject/infrastructure-playbook/commit/d4f94ab28a7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M jetstreamiuenv/group_vars/slurmclients.yml M jetstreamiuenv/inventory M jetstreamtaccenv/group_vars/slurmclients.yml M jetstreamtaccenv/inventory Log Message: ----------- Jetstream GO!

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[galaxyproject/galaxy] ca5f60: Fix tool action redirects for non-default tools di...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ca5f6053c7b13fa8f631f0a96f78a8aac544175c https://github.com/galaxyproject/galaxy/commit/ca5f6053c7b13fa8f631f0a96f78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Fix tool action redirects for non-default tools displaying tool forms Commit: f70a2b024237dcc797665134e311e7ada7602b1c https://github.com/galaxyproject/galaxy/commit/f70a2b024237dcc797665134e311… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Merge pull request #2211 from guerler/fix_nondefault_000 [16.04] Fix tool action redirect url for non-default tools Commit: 971613404c68a3c3e8ee1ca8bc34693714c4ae17 https://github.com/galaxyproject/galaxy/commit/971613404c68a3c3e8ee1ca8bc34… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Avoid reset of cursor position for input fields during manual entry Commit: 2734c2c4835ae725440c25314034f3dd296b00f1 https://github.com/galaxyproject/galaxy/commit/2734c2c4835ae725440c25314034… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Merge pull request #2218 from guerler/fix_cursor_001 [16.04] Avoid reset of cursor position for input fields during manual entry Commit: c563d37bfd8da83fcd090067b32e3421b35802fb https://github.com/galaxyproject/galaxy/commit/c563d37bfd8da83fcd090067b32e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/ui/ui-misc.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/ui/ui-misc.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/tool/tool-form.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge branch 'release_16.04' into dev Compare: https://github.com/galaxyproject/galaxy/compare/266a45ad7100...c563d37bfd8d

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[galaxyproject/galaxy] 971613: Avoid reset of cursor position for input fields du...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 971613404c68a3c3e8ee1ca8bc34693714c4ae17 https://github.com/galaxyproject/galaxy/commit/971613404c68a3c3e8ee1ca8bc34… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Avoid reset of cursor position for input fields during manual entry Commit: 2734c2c4835ae725440c25314034f3dd296b00f1 https://github.com/galaxyproject/galaxy/commit/2734c2c4835ae725440c25314034… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.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/ui/ui-misc.js Log Message: ----------- Merge pull request #2218 from guerler/fix_cursor_001 [16.04] Avoid reset of cursor position for input fields during manual entry Compare: https://github.com/galaxyproject/galaxy/compare/f70a2b024237...2734c2c4835a

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[galaxyproject/galaxy] ef12ae: Test fix for christ-h's french language date abbre...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy 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 Compare: https://github.com/galaxyproject/galaxy/compare/5aefe1b193d8...3907d83abe98

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[galaxyproject/galaxy] c04fcc: Fix bug when determining locale
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c04fcc86b48ce7bfeed793e45d1b5418d9c11a55 https://github.com/galaxyproject/galaxy/commit/c04fcc86b48ce7bfeed793e45d1b… Author: yangyuanjie <jayyoung(a)yangyuanjiedeMacBook-Pro.local> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/utils/localization.js Log Message: ----------- Fix bug when determining locale Commit: 9cd168bbabf1347a02a435cc1186fdf4aac183bb https://github.com/galaxyproject/galaxy/commit/9cd168bbabf1347a02a435cc1186… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M static/maps/utils/localization.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/localization.js Log Message: ----------- make client Commit: 18dcf10aca7b65f2be2661886ddee86c6bb2c6c7 https://github.com/galaxyproject/galaxy/commit/18dcf10aca7b65f2be2661886dde… Author: xiaojay <xiaojay(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M static/maps/utils/localization.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/localization.js Log Message: ----------- Merge pull request #1 from dannon/xiaojay_dev Building the client Commit: 266a45ad71002e391b646da24aa40eccda0f21cc https://github.com/galaxyproject/galaxy/commit/266a45ad71002e391b646da24aa4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/utils/localization.js M static/maps/utils/localization.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/utils/localization.js Log Message: ----------- Merge pull request #2213 from xiaojay/dev Fix bug when determining locale Compare: https://github.com/galaxyproject/galaxy/compare/be588228869a...266a45ad7100

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[galaxyproject/galaxy] ca5f60: Fix tool action redirects for non-default tools di...
by GitHub 21 Apr '16

21 Apr '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: ca5f6053c7b13fa8f631f0a96f78a8aac544175c https://github.com/galaxyproject/galaxy/commit/ca5f6053c7b13fa8f631f0a96f78… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Fix tool action redirects for non-default tools displaying tool forms Commit: f70a2b024237dcc797665134e311e7ada7602b1c https://github.com/galaxyproject/galaxy/commit/f70a2b024237dcc797665134e311… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-21 (Thu, 21 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tool/tool-form.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/tool/tool-form.js Log Message: ----------- Merge pull request #2211 from guerler/fix_nondefault_000 [16.04] Fix tool action redirect url for non-default tools Compare: https://github.com/galaxyproject/galaxy/compare/e88e615d6e6b...f70a2b024237

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 20 Apr '16

20 Apr '16

Branch: refs/heads/master 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: 774487ddcc9c0e793b6b15b26c971c3df5822644 https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5 https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.js.map M static/scripts/mvc/citation/citation-model.js Log Message: ----------- Merge pull request #1884 from carlfeberhard/release_15.10 [15.10] Fix citation-model to fail silently/gracefully Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4 https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1972 from carlfeberhard/release_15.10 [15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i… 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. Commit: 449098d8b14b45269be106f6410c0b9145c51d50 https://github.com/galaxyproject/galaxy/commit/449098d8b14b45269be106f6410c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-30 (Wed, 30 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- upgrade mercurial wheel to latest (fixing CVE issues) Commit: dc4d4cbce7b18b33ff09f722d58a551c6f024b7a https://github.com/galaxyproject/galaxy/commit/dc4d4cbce7b18b33ff09f722d58a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#depre… Commit: 7d08d1b0699a9e2adfa314af3e8324e257254ce0 https://github.com/galaxyproject/galaxy/commit/7d08d1b0699a9e2adfa314af3e83… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Specify default value when getting disable_push Commit: a560ad8999eca1137aafa466ae07683ef9f6d9d3 https://github.com/galaxyproject/galaxy/commit/a560ad8999eca1137aafa466ae07… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_clone.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Update Tool Shed tests after disabling 'hg push' Commit: 28b5dd36832642b5ae519790c25fc2d15da11ca9 https://github.com/galaxyproject/galaxy/commit/28b5dd36832642b5ae519790c25f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- add TS test for disabled hg push Commit: 0bcc7e37e1d94259c6b5c29ab7e8041e4228d05d https://github.com/galaxyproject/galaxy/commit/0bcc7e37e1d94259c6b5c29ab7e8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_clone.py Log Message: ----------- rename test to reflect insides Commit: 193eeaa60674eaa1badb65f74cb77dcb331b179b https://github.com/galaxyproject/galaxy/commit/193eeaa60674eaa1badb65f74cb7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2056 from martenson/1601-disable-push [16.01] retroactively disable Mercurial push API in TS Commit: 90b95dc665bd736a21bd16d2852caf5c23bb83c4 https://github.com/galaxyproject/galaxy/commit/90b95dc665bd736a21bd16d2852c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-31 (Thu, 31 Mar 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #2043 from martenson/update_mercurial_wheel [16.01] upgrade mercurial wheel to latest (fixing CVE issues) Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29 https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- workaround for error message in case original toolshed had been disabled Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9 https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-04 (Mon, 04 Apr 2016) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #2072 from mvdbeek/backport_1738 [16.01] backport #1738 Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Show sections in workflow run Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109 https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Patch in visual separation of section parameters Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-05 (Tue, 05 Apr 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2092 from erasche/workflow-section-backport [16.01] Workflow section fix backport Commit: 9ecf99c227466a586a6299e37555655f5ff79a25 https://github.com/galaxyproject/galaxy/commit/9ecf99c227466a586a6299e37555… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- make dependencies browsable again it would be denied previously as the dependency folder is outside of the repository (symlink protection) Commit: 0882b4d8fb31752f1fa8c963c3f260f975c918f7 https://github.com/galaxyproject/galaxy/commit/0882b4d8fb31752f1fa8c963c3f2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-06 (Wed, 06 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- use proper method for detecting admin Commit: 50268cb8ca4a5f812346a71cc640141781f22a3d https://github.com/galaxyproject/galaxy/commit/50268cb8ca4a5f812346a71cc640… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-07 (Thu, 07 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- fix missing call; add docs and refactor a bit Commit: 455113d182236a0fec880db296b746a413a8edc4 https://github.com/galaxyproject/galaxy/commit/455113d182236a0fec880db296b7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-08 (Fri, 08 Apr 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #2101 from martenson/fix-browsing-dependencies [16.01] make dependencies browsable again Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379 https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- mention planemo in the error message for disabled TS pushing rephrase to Norwegian Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76 https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-11 (Mon, 11 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #2114 from martenson/planemo-mention [16.01] mention planemo in the error message for disabled TS pushing Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92 https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. Fix #2135. Commit: 2ebe9405106dfc16504e3b6f775425634bb4691f https://github.com/galaxyproject/galaxy/commit/2ebe9405106dfc16504e3b6f7754… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/layout/page.js Log Message: ----------- load options from config, not from options Commit: ad952a4b8d7501d0df48e44d7c966ff22f9a63c4 https://github.com/galaxyproject/galaxy/commit/ad952a4b8d7501d0df48e44d7c96… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2016-04-12 (Tue, 12 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.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/layout/page.js Log Message: ----------- Merge pull request #2139 from martenson/fix-inactivity [16.01] load options from config, not from options Commit: 1e3b3a15581ecd62e78999f6be9e74d9e7cfbc65 https://github.com/galaxyproject/galaxy/commit/1e3b3a15581ecd62e78999f6be9e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-12 (Tue, 12 Apr 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 the value passed to Masthead as options were options.config before Commit: 4c2bca51171efff42e2852bfa59a91d5acee3e73 https://github.com/galaxyproject/galaxy/commit/4c2bca51171efff42e2852bfa59a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 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 #2141 from martenson/fix-sideeffect [16.01] fix the value passed to Masthead as options were options.config before Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565 https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-13 (Wed, 13 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- port of middleware fix for TS (#2106) Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170 https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #2154 from martenson/port-middleware-fix [16.01] Port middleware fix Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35 https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/history/multi-panel.js Log Message: ----------- Multi-history: open rerun button in new tab Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge 'release_15.10' with 'release_16.01' Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fix bad merge: when HTTP_GX_SECRET is None Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3 https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M lib/galaxy/web/framework/middleware/remoteuser.py M static/maps/mvc/citation/citation-model.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/citation/citation-model.js M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #2169 from carlfeberhard/release_16.01 [16.01] Merge 15.10 with 16.01 Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3 https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-14 (Thu, 14 Apr 2016) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 [16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3 https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Place $headers before integrity_check PBS needs the resource selection (which will be filled in using $headers) to appear before anything else (except the shebang), so this changes the order. Commit: 434321915a61f53cd668170da076251a8c15889f https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Log Message: ----------- Use "$NCPUS" if defined to set GALAXY_SLOTS On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the hostname of the nodes the task runs on. But we do have "$NCPUS" with the correct number of CPUS. Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #2174 from mvdbeek/reorder_job_template [16.01] Backport #2146 #2145 Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.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/history/multi-panel.js Log Message: ----------- Merge #2167 manually to resolve conflicts. Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60 https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client. Commit: b95cca862cae9cf7e78370fd68ea5f530fb8194f https://github.com/galaxyproject/galaxy/commit/b95cca862cae9cf7e78370fd68ea… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-15 (Fri, 15 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- always fetch new permissions as we are reusing the view Commit: e2f88296f8454e9195ad1a6f2d4c9c9ade40ee77 https://github.com/galaxyproject/galaxy/commit/e2f88296f8454e9195ad1a6f2d4c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-04-18 (Mon, 18 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js Log Message: ----------- Merge pull request #2176 from martenson/fix-permissions-caching [16.01] libraries: always fetch new permissions as we are reusing the view Commit: cfb8ed32693d6aad0ef26af7af7171e0e8c3ee04 https://github.com/galaxyproject/galaxy/commit/cfb8ed32693d6aad0ef26af7af71… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- UI, citations: fix bad merge from 15.10 774487d created a difference between the imported name and the one used. Commit: 3737fc9487ad25ba09960e0d7858d4c15a3087bf https://github.com/galaxyproject/galaxy/commit/3737fc9487ad25ba09960e0d7858… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-19 (Tue, 19 Apr 2016) Changed paths: M client/galaxy/scripts/mvc/citation/citation-model.js M static/maps/mvc/citation/citation-model.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/citation/citation-model.js Log Message: ----------- Merge pull request #2198 from carlfeberhard/fix.citations-again [16.01] UI, citations: fix bad merge from 15.10 Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Make client, somehow this got out of sync. Commit: 5aefe1b193d866185958645b832f2d731f933c01 https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #2207 from dannon/release_16.01 [16.01] Rebuild client, maps were out of sync. Commit: b79474083b08860923f7f28fc1e7442b53f925db https://github.com/galaxyproject/galaxy/commit/b79474083b08860923f7f28fc1e7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-04-20 (Wed, 20 Apr 2016) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/tool_shed/util/shed_util_common.py M static/maps/layout/page.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/library/library-dataset-view.js.map M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-library-view.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/layout/page.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-folder-view.js M static/scripts/mvc/library/library-library-view.js M templates/webapps/galaxy/galaxy.panels.mako M templates/webapps/galaxy/workflow/run.mako M test/tool_shed/base/twilltestcase.py A test/tool_shed/functional/test_0310_hg_api_features.py R test/tool_shed/functional/test_0310_hg_push_from_api.py Log Message: ----------- Merge pull request #2206 from dannon/master Sanity check of master update. Compare: https://github.com/galaxyproject/galaxy/compare/7c94ac8d93b8...b79474083b08

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