November 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 39fe6b: Rebuild styles, fixes history panel green being wr...
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 39fe6b44bfbab9f490524dff902ceb80bc52a2ee https://github.com/galaxyproject/galaxy/commit/39fe6b44bfbab9f490524dff902c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Rebuild styles, fixes history panel green being wrong. Commit: 65301bb9c85a1c09fdd36890b68593b320fcf3e7 https://github.com/galaxyproject/galaxy/commit/65301bb9c85a1c09fdd36890b685… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M static/style/blue/autocomplete_tagging.css M static/style/blue/base.css M static/style/blue/embed_item.css M static/style/blue/iphone.css M static/style/blue/library.css M static/style/blue/trackster.css Log Message: ----------- Merge pull request #1102 from dannon/style_rebuild Rebuild styles, fixes history panel green being wrong. Compare: https://github.com/galaxyproject/galaxy/compare/d2d2ff12775b...65301bb9c85a

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[galaxyproject/galaxy] b19e71: Update run_tests.sh help for #844.
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b19e71ec465c7145840acf684f8f09eeebb99b5a https://github.com/galaxyproject/galaxy/commit/b19e71ec465c7145840acf684f8f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Update run_tests.sh help for #844. Commit: d2d2ff12775bc630ff6705c7989fe84fed9cbdbb https://github.com/galaxyproject/galaxy/commit/d2d2ff12775bc630ff6705c7989f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #1101 from nsoranzo/run_tests_sh Update run_tests.sh help for #844. Compare: https://github.com/galaxyproject/galaxy/compare/13eb47e78933...d2d2ff12775b

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[galaxyproject/galaxy] daf505: Point organization document to issue handling for ...
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: daf505eaccd751a4ed6d34f42f32cd890ad162a5 https://github.com/galaxyproject/galaxy/commit/daf505eaccd751a4ed6d34f42f32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Point organization document to issue handling for binding procedure Commit: bc217b6a278cdb7d5078d24b79db8116e9405239 https://github.com/galaxyproject/galaxy/commit/bc217b6a278cdb7d5078d24b79db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-22 (Thu, 22 Oct 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Place correctly after the last section. Commit: 9bbb3b97bd32a83303168a839a68070c822d04c4 https://github.com/galaxyproject/galaxy/commit/9bbb3b97bd32a83303168a839a68… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-23 (Fri, 23 Oct 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Fix link from org to issues. Commit: 13eb47e789336f4ebfe0923ae07f0db81afd2d63 https://github.com/galaxyproject/galaxy/commit/13eb47e789336f4ebfe0923ae07f… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-16 (Mon, 16 Nov 2015) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Merge pull request #1020 from dannon/issue_procedure [PROCEDURES] Issue procedure linkage Compare: https://github.com/galaxyproject/galaxy/compare/cfe45d8e0c35...13eb47e78933

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[galaxyproject/galaxy] 1aecca: Fix API installation of tool_dependencies
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aecca7889681ad9518e26e2a62b470809d2cdd1 https://github.com/galaxyproject/galaxy/commit/1aecca7889681ad9518e26e2a62b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: 7e67368424a718f2e156b961aaf0a1a9672df9ce https://github.com/galaxyproject/galaxy/commit/7e67368424a718f2e156b961aaf0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Don't fail if a repository is already installed If an repository is already installed `installed_tool_shed_repositories` is None and this does not work with map. Commit: 38f0ed5d043951cc06abeaab9bbf1f4d888e372a https://github.com/galaxyproject/galaxy/commit/38f0ed5d043951cc06abeaab9bbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Improve the API attributes on parameters page. Make clear what API ID is and add display of API value for job. Commit: bbe7fbe38c57fd89434eea850621770a1d355231 https://github.com/galaxyproject/galaxy/commit/bbe7fbe38c57fd89434eea850621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1098 from jmchilton/show_param Improve the API attributes on parameters page. Commit: a26526b085c29d41f5662b7f80dee7e3e7a7c294 https://github.com/galaxyproject/galaxy/commit/a26526b085c29d41f5662b7f80de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1094 from bgruening/fix_api_ts_installation Fix api TS installation Commit: cfe45d8e0c357cbe191a346a2ae05e1625bb5010 https://github.com/galaxyproject/galaxy/commit/cfe45d8e0c357cbe191a346a2ae0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Merge pull request #1095 from bgruening/ts_api_fail_if_installed Don't fail if a repository is already installed Compare: https://github.com/galaxyproject/galaxy/compare/3ba139fe1bf8...cfe45d8e0c35

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[galaxyproject/galaxy]
by GitHub 17 Nov '15

17 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 7e6736: Don't fail if a repository is already installed
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e67368424a718f2e156b961aaf0a1a9672df9ce https://github.com/galaxyproject/galaxy/commit/7e67368424a718f2e156b961aaf0… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Don't fail if a repository is already installed If an repository is already installed `installed_tool_shed_repositories` is None and this does not work with map. Commit: cfe45d8e0c357cbe191a346a2ae05e1625bb5010 https://github.com/galaxyproject/galaxy/commit/cfe45d8e0c357cbe191a346a2ae0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py Log Message: ----------- Merge pull request #1095 from bgruening/ts_api_fail_if_installed Don't fail if a repository is already installed Compare: https://github.com/galaxyproject/galaxy/compare/a26526b085c2...cfe45d8e0c35

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[galaxyproject/galaxy] 1aecca: Fix API installation of tool_dependencies
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1aecca7889681ad9518e26e2a62b470809d2cdd1 https://github.com/galaxyproject/galaxy/commit/1aecca7889681ad9518e26e2a62b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Fix API installation of tool_dependencies This should fix an installation issue with tool_dependencies via the API. Tool dependency repositories to not have any tools specified and with this no metadata associated. It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d44884… So I think this should be part of 15.10. Thanks to Greg for fixing this one. Commit: a26526b085c29d41f5662b7f80dee7e3e7a7c294 https://github.com/galaxyproject/galaxy/commit/a26526b085c29d41f5662b7f80de… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Merge pull request #1094 from bgruening/fix_api_ts_installation Fix api TS installation Compare: https://github.com/galaxyproject/galaxy/compare/bbe7fbe38c57...a26526b085c2

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[galaxyproject/galaxy] 38f0ed: Improve the API attributes on parameters page.
by GitHub 16 Nov '15

16 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 38f0ed5d043951cc06abeaab9bbf1f4d888e372a https://github.com/galaxyproject/galaxy/commit/38f0ed5d043951cc06abeaab9bbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Improve the API attributes on parameters page. Make clear what API ID is and add display of API value for job. Commit: bbe7fbe38c57fd89434eea850621770a1d355231 https://github.com/galaxyproject/galaxy/commit/bbe7fbe38c57fd89434eea850621… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-15 (Sun, 15 Nov 2015) Changed paths: M templates/show_params.mako Log Message: ----------- Merge pull request #1098 from jmchilton/show_param Improve the API attributes on parameters page. Compare: https://github.com/galaxyproject/galaxy/compare/3ba139fe1bf8...bbe7fbe38c57

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[galaxyproject/galaxy] 75e7e4: Fix 500 error when attempting to update installed ...
by GitHub 15 Nov '15

15 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 75e7e4c2cf7a0cb18b8096c8119e4b0cb207e2a3 https://github.com/galaxyproject/galaxy/commit/75e7e4c2cf7a0cb18b8096c8119e… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 7150983aab78e4ceb71f8ad2592369523899d768 https://github.com/galaxyproject/galaxy/commit/7150983aab78e4ceb71f8ad25923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1093 from martenson/release_15.10 [15.10] Fix 500 error when attempting to update installed repository. Compare: https://github.com/galaxyproject/galaxy/compare/64b084067c73...7150983aab78

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[galaxyproject/galaxy] 7c45bf: Fix 500 error when attempting to update installed ...
by GitHub 15 Nov '15

15 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c45bf13fad2d60fbee8be409c6879af2ebc25d1 https://github.com/galaxyproject/galaxy/commit/7c45bf13fad2d60fbee8be409c68… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Fix 500 error when attempting to update installed repository. Commit: 321b64d8dcc1917eb107e46124cdb945c5005511 https://github.com/galaxyproject/galaxy/commit/321b64d8dcc1917eb107e46124cd… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Ensure that invalid parameters don't break things. Commit: 87f35ea9752a37da76595db1fee481c391ee686b https://github.com/galaxyproject/galaxy/commit/87f35ea9752a37da76595db1fee4… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-11-13 (Fri, 13 Nov 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Use preexisting library to parse query string. Commit: 3ba139fe1bf8a40df647282a9884eae543a656bc https://github.com/galaxyproject/galaxy/commit/3ba139fe1bf8a40df647282a9884… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-14 (Sat, 14 Nov 2015) Changed paths: M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py Log Message: ----------- Merge pull request #1082 from davebx/hg_middleware Fix 500 error when attempting to update installed repository. Compare: https://github.com/galaxyproject/galaxy/compare/f1abf1e9ab4d...3ba139fe1bf8

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