- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 6182e0: Visualizations registry: always set 'tests' for a ...
by GitHub 13 Oct '15

13 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6182e0d2b90ea46c3eb095211b3c48690f275d0c https://github.com/galaxyproject/galaxy/commit/6182e0d2b90ea46c3eb095211b3c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Visualizations registry: always set 'tests' for a plugin, defaulting to an empty list Commit: 9808acf5aede1f94c3054a09d761a32ceeb577b2 https://github.com/galaxyproject/galaxy/commit/9808acf5aede1f94c3054a09d761… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/visualization/plugins/config_parser.py Log Message: ----------- Merge pull request #908 from carlfeberhard/fix.vis-config-tests Visualizations registry: always set 'tests' for a plugin, defaulting … Compare: https://github.com/galaxyproject/galaxy/compare/a29d05846026...9808acf5aede

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[galaxyproject/galaxy] 08f1e7: Add pdf datatype to list of uploadable files
by GitHub 13 Oct '15

13 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 08f1e7b3ade171de693b014e17e5921974fd3472 https://github.com/galaxyproject/galaxy/commit/08f1e7b3ade171de693b014e17e5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add pdf datatype to list of uploadable files Commit: a29d0584602641175ceb685f7fcaddda472d02b3 https://github.com/galaxyproject/galaxy/commit/a29d0584602641175ceb685f7fca… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #901 from guerler/pdf_upload_000 Avoid confusion by adding the pdf datatype to the list of uploadable file types Compare: https://github.com/galaxyproject/galaxy/compare/52d4d0ef02d0...a29d05846026

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[galaxyproject/galaxy] 60a1b4: make lib search case insensitive
by GitHub 12 Oct '15

12 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 60a1b45704c4794e6fcac2e9ab6001484a801ca6 https://github.com/galaxyproject/galaxy/commit/60a1b45704c4794e6fcac2e9ab60… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-model.js M static/maps/mvc/library/library-model.js.map M static/scripts/mvc/library/library-model.js Log Message: ----------- make lib search case insensitive Commit: 2d4bd2e6f5c64162ab2c1de6d6b1e338bafb4b16 https://github.com/galaxyproject/galaxy/commit/2d4bd2e6f5c64162ab2c1de6d6b1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarytoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- fix the ordering and margins of lib toolbar items Commit: 39f5b7adf1cb835eed7b450806b249200c2a9cbe https://github.com/galaxyproject/galaxy/commit/39f5b7adf1cb835eed7b450806b2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- show proper message when search has no results Commit: 775ee33d4dbf7cb763e9f25430aae645d2df4c65 https://github.com/galaxyproject/galaxy/commit/775ee33d4dbf7cb763e9f25430aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- fix options default order to fix bug with improper page being rendered also add missing comma for previous commit Commit: fe8dbd8183fe5706e041686ee57a683d1fd63c9e https://github.com/galaxyproject/galaxy/commit/fe8dbd8183fe5706e041686ee57a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- fix problems with multiple bindings of view events; drop attempts at caching the libraries - need to study more for that Commit: 251f390f7c45f5d02af90f01f7b892b207950cb6 https://github.com/galaxyproject/galaxy/commit/251f390f7c45f5d02af90f01f7b8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the ordering of folder controls to match library's also fix the active area of 'include deleted' checkbox Commit: 6c5f6e3f692c2b151afab39126a068f56971708d https://github.com/galaxyproject/galaxy/commit/6c5f6e3f692c2b151afab39126a0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/library/library-model.js M client/galaxy/style/less/library.less M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/maps/mvc/library/library-model.js.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/library/library-model.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #878 from martenson/datalib-fixes-release [15.10] Release Fixes for Data Libraries Compare: https://github.com/galaxyproject/galaxy/compare/38b9ca3400ea...6c5f6e3f692c

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[galaxyproject/usegalaxy-playbook] 949feb: update MTS to latest 15.10
by GitHub 12 Oct '15

12 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 949feb516c4bba924dd77dc9480480fadb3c9f55 https://github.com/galaxyproject/usegalaxy-playbook/commit/949feb516c4bba92… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS to latest 15.10

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[galaxyproject/usegalaxy-playbook] 003e6b: update TTS
by GitHub 12 Oct '15

12 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 003e6b6702432db86353ac88210f9f829dcfd19d https://github.com/galaxyproject/usegalaxy-playbook/commit/003e6b6702432db8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] 611366: replace exit() with quit(), this is more portable
by GitHub 12 Oct '15

12 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6113663f91e18a2c4e2189fb008a1e1478684cf9 https://github.com/galaxyproject/galaxy/commit/6113663f91e18a2c4e2189fb008a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- replace exit() with quit(), this is more portable Commit: 52d4d0ef02d096a09288c75ebb37dadee1012bad https://github.com/galaxyproject/galaxy/commit/52d4d0ef02d096a09288c75ebb37… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-12 (Mon, 12 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #893 from bgruening/R_return replace exit() with quit(), this is more portable Compare: https://github.com/galaxyproject/galaxy/compare/19f574939da9...52d4d0ef02d0

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[galaxyproject/galaxy] a6efdc: fix for strange package names
by GitHub 11 Oct '15

11 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a6efdc5a2b41979ae824611abdb17a633ed32aaf https://github.com/galaxyproject/galaxy/commit/a6efdc5a2b41979ae824611abdb1… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-10-10 (Sat, 10 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- fix for strange package names Commit: 19f574939da9d4ce361563498289ea8d1732cf08 https://github.com/galaxyproject/galaxy/commit/19f574939da9d4ce361563498289… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-11 (Sun, 11 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #889 from bgruening/ROOT_DIR_fix fix for strange package names Compare: https://github.com/galaxyproject/galaxy/compare/858eed632a6e...19f574939da9

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[galaxyproject/galaxy] fea863: Add a workaround to return a proper error code if ...
by GitHub 11 Oct '15

11 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fea863081ce8a41bbd10c8d26c2409c660e0ad88 https://github.com/galaxyproject/galaxy/commit/fea863081ce8a41bbd10c8d26c24… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-10-02 (Fri, 02 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Add a workaround to return a proper error code if a R packge fails to install. Commit: 858eed632a6e8228ab71c02c2d7b74f3f9ea5dcd https://github.com/galaxyproject/galaxy/commit/858eed632a6e8228ab71c02c2d7b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-11 (Sun, 11 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #892 from bgruening/setupRinstall-fail Add a workaround to return a proper error code Compare: https://github.com/galaxyproject/galaxy/compare/408c82c43d6d...858eed632a6e

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[galaxyproject/galaxy] 45763b: Use common exceptions in tools
by GitHub 10 Oct '15

10 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45763bf85e2a868476b2807bac1ddf92be844f76 https://github.com/galaxyproject/galaxy/commit/45763bf85e2a868476b2807bac1d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Use common exceptions in tools Commit: 408c82c43d6d05650668067b82aee8e8ece7d678 https://github.com/galaxyproject/galaxy/commit/408c82c43d6d05650668067b82ae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-10 (Sat, 10 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/tools/__init__.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #874 from guerler/tool_execution_001 Use common exceptions in tools Compare: https://github.com/galaxyproject/galaxy/compare/fae21e30f56e...408c82c43d6d

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[galaxyproject/usegalaxy-playbook] ad9674: Main: virtualenv and module fixes for Stampede
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ad96740f1a88fec30aea159dc810a06f7398edaf https://github.com/galaxyproject/usegalaxy-playbook/commit/ad96740f1a88fec3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Main: virtualenv and module fixes for Stampede

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