- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 120ec6: Fix command quoting and remove size from text inpu...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 120ec61264dadb90b0386e46bd4c33a2f6481c52 https://github.com/galaxyproject/galaxy/commit/120ec61264dadb90b0386e46bd4c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Fix command quoting and remove size from text input for Cut tool. Commit: cf59e8bd3c52f52ae717ca9755e6b10f48382b07 https://github.com/galaxyproject/galaxy/commit/cf59e8bd3c52f52ae717ca9755e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/filters/cutWrapper.xml Log Message: ----------- Merge pull request #913 from blankenberg/cut_15.10 [15.10] Fix command quoting and remove size from text input for Cut tool. Compare: https://github.com/galaxyproject/galaxy/compare/ee42fd053191...cf59e8bd3c52

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[galaxyproject/galaxy] c64f27: Only return repository if it is not None ( This ha...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c64f27e014ea4f79b45c2a7172ccee10edf11ec7 https://github.com/galaxyproject/galaxy/commit/c64f27e014ea4f79b45c2a7172cc… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2015-10-10 (Sat, 10 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py Log Message: ----------- Only return repository if it is not None ( This happends for the repository that we try to repair). Add the repository to be repaired to installed_repository list. Commit: 744ed8cd4c80c742d12762202f52795b56f0fcf0 https://github.com/galaxyproject/galaxy/commit/744ed8cd4c80c742d12762202f52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/tool_shed/galaxy_install/repair_repository_manager.py Log Message: ----------- Merge pull request #891 from mvdbeek/repair_repository_id_fix Only return repository if it is not None ( This happens for the repo… Compare: https://github.com/galaxyproject/galaxy/compare/6c95ef9d969a...744ed8cd4c80

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[galaxyproject/galaxy] ad2045: Fix output to print values and not hash key
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: ad20452340d052570c1b3203259d10e1ad94a236 https://github.com/galaxyproject/galaxy/commit/ad20452340d052570c1b3203259d… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Fix output to print values and not hash key Commit: ad4458a458d7ccb5238094ab3d1967072b5a0b76 https://github.com/galaxyproject/galaxy/commit/ad4458a458d7ccb5238094ab3d19… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Revert to previous changes if using rpy2 Commit: 0ec1b17794d53ae1a535b00f13d955c62f702a94 https://github.com/galaxyproject/galaxy/commit/0ec1b17794d53ae1a535b00f13d9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Update list comprehension to go through headings instead of summary so that we output in the order we want. Commit: 50c27ace2c6eb260b88aafac72997cfa06ca6c13 https://github.com/galaxyproject/galaxy/commit/50c27ace2c6eb260b88aafac7299… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #885 from ericenns/fix_gsummary_in_release_15.07 [15.07] Fix gsummary in release 15.07 Compare: https://github.com/galaxyproject/galaxy/compare/76fcde327468...50c27ace2c6e

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[galaxyproject/galaxy] b47084: UI, histories: fix multiview button to be logged-i...
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: b470843c89af119b9800d6fb68323338c7020fb6 https://github.com/galaxyproject/galaxy/commit/b470843c89af119b9800d6fb6832… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- UI, histories: fix multiview button to be logged-in users only Commit: 99fab6f342f6f50536b1a5544b8b07f769805497 https://github.com/galaxyproject/galaxy/commit/99fab6f342f6f50536b1a5544b8b… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/list/list-panel.js Log Message: ----------- UI, histories: on first history search, use current searchFor value at callback and not value when ajax began Commit: 34a11d1187127face6dd0c780051458b2b5d7430 https://github.com/galaxyproject/galaxy/commit/34a11d1187127face6dd0c780051… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: fix default empty message for lazy loaded panels in multi-view Commit: 41069e8ba6dcd6328864eabb104e36a2a70e6140 https://github.com/galaxyproject/galaxy/commit/41069e8ba6dcd6328864eabb104e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: fix/reverse order for drag and drop dataset copy Commit: 03c7aae512d010a3100a547af3c194e6f8957e35 https://github.com/galaxyproject/galaxy/commit/03c7aae512d010a3100a547af3c1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M client/galaxy/style/less/list-item.less M static/style/blue/base.css Log Message: ----------- UI, histories: disable user-select on dataset selectors to prevent text select/highlight when using shift to select a range Commit: ee42fd05319171a79791803d5c0adc168ef2cced https://github.com/galaxyproject/galaxy/commit/ee42fd05319171a79791803d5c0a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/style/less/list-item.less M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/list/list-panel.js.map M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/list/list-panel.js M static/style/blue/base.css Log Message: ----------- Merge pull request #910 from carlfeberhard/release_15.10 [15.10] Some minor fixes to the history UI Compare: https://github.com/galaxyproject/galaxy/compare/6c5f6e3f692c...ee42fd053191

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[galaxyproject/galaxy] daffa9: Correct newly broken condor runner
by GitHub 14 Oct '15

14 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: daffa942148da1d8aea1eefe795564cc7e753a06 https://github.com/galaxyproject/galaxy/commit/daffa942148da1d8aea1eefe7955… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-13 (Tue, 13 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Correct newly broken condor runner Commit: 6c95ef9d969ac1d6ac170133e1a79c23d93ed2f2 https://github.com/galaxyproject/galaxy/commit/6c95ef9d969ac1d6ac170133e1a7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M lib/galaxy/jobs/runners/condor.py Log Message: ----------- Merge pull request #909 from erasche/condor-runner-issue Correct newly broken condor runner Compare: https://github.com/galaxyproject/galaxy/compare/9808acf5aede...6c95ef9d969a

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[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 09 Oct '15

09 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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[galaxyproject/usegalaxy-playbook] a17ff1: Test mutable configs
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a17ff1ef2c59d335cc15521964e7ea55bbbff59b https://github.com/galaxyproject/usegalaxy-playbook/commit/a17ff1ef2c59d335… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml 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 Log Message: ----------- Test mutable configs Commit: 89cbe794153c334a723ff0b80f9db8aa07bd3f84 https://github.com/galaxyproject/usegalaxy-playbook/commit/89cbe794153c334a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test Commit: 6757018a7c6397365f2cc459db853857c6bb5b1a https://github.com/galaxyproject/usegalaxy-playbook/commit/6757018a7c639736… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Test: Ensure Pulsar jobs use Galaxy's venv, not Pulsar's. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3b6a3b14c56f...…

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[galaxyproject/galaxy] 31c89e: UI, Collections: allow expansion to fetch details ...
by GitHub 09 Oct '15

09 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 31c89ea29c2c504878f336d90dfcf320b873b2ee https://github.com/galaxyproject/galaxy/commit/31c89ea29c2c504878f336d90dfc… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- UI, Collections: allow expansion to fetch details for DatasetDCEs (assuming they're HDAs); move rerunnable and creating_job fetch to HDAs Commit: 69cd5a98dcda30771ce78118ebd3a934dfb09c65 https://github.com/galaxyproject/galaxy/commit/69cd5a98dcda30771ce78118ebd3… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-10-06 (Tue, 06 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js Log Message: ----------- Merge pull request #854 from carlfeberhard/release_15.10 [15.10] UI, Collections: allow expansion to fetch details for DatasetDCEs (as… Commit: 4705409d386f6cabe1874ac044617d6ed226a80e https://github.com/galaxyproject/galaxy/commit/4705409d386f6cabe1874ac04461… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a0ad2b75c29eca2c33ccfcdd4aa4a834c06c5265 https://github.com/galaxyproject/galaxy/commit/a0ad2b75c29eca2c33ccfcdd4aa4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #873 from erasche/api-key-backpatch [release_15.10] Expose all API keys to admins under REMOTE_USER Commit: 90506ba1c6b83731cf5e11badabfde1f8d3e34c4 https://github.com/galaxyproject/galaxy/commit/90506ba1c6b83731cf5e11badabf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Fix for no longer being able to access data managers. Have datamanager links point to root with tool_id provided while targeting a new window. Commit: 38b9ca3400eaf482c50c6224438d3341241453c1 https://github.com/galaxyproject/galaxy/commit/38b9ca3400eaf482c50c6224438d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #879 from blankenberg/datamanager-fix [15.10] Fix for no longer being able to access data managers. Commit: fae21e30f56e5a1e92aa80f58daa684eeb87aaa9 https://github.com/galaxyproject/galaxy/commit/fae21e30f56e5a1e92aa80f58daa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/history/hda-li-edit.js M static/maps/mvc/collection/collection-li-edit.js.map M static/maps/mvc/collection/collection-li.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/history/hda-li-edit.js.map M static/scripts/mvc/collection/collection-li-edit.js M static/scripts/mvc/collection/collection-li.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/history/hda-li-edit.js M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge branch 'release_15.10' into dev Conflicts: lib/galaxy/web/framework/middleware/remoteuser.py Compare: https://github.com/galaxyproject/galaxy/compare/f10047c4d31e...fae21e30f56e

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[galaxyproject/galaxy] 90506b: Fix for no longer being able to access data manage...
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 90506ba1c6b83731cf5e11badabfde1f8d3e34c4 https://github.com/galaxyproject/galaxy/commit/90506ba1c6b83731cf5e11badabf… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Fix for no longer being able to access data managers. Have datamanager links point to root with tool_id provided while targeting a new window. Commit: 38b9ca3400eaf482c50c6224438d3341241453c1 https://github.com/galaxyproject/galaxy/commit/38b9ca3400eaf482c50c6224438d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/data_manager/index.mako M templates/webapps/galaxy/data_manager/view_job.mako Log Message: ----------- Merge pull request #879 from blankenberg/datamanager-fix [15.10] Fix for no longer being able to access data managers. Compare: https://github.com/galaxyproject/galaxy/compare/a0ad2b75c29e...38b9ca3400ea

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[galaxyproject/galaxy] c72618: Slight tweak to sidebar section naming from 'secur...
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c72618680287d9affd56f5c4434ef7a9b9525e8d https://github.com/galaxyproject/galaxy/commit/c72618680287d9affd56f5c4434e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Slight tweak to sidebar section naming from 'security' to 'user management', for users, groups, roles, api keys Commit: f10047c4d31ef44ca6be03894224ecc36d44627e https://github.com/galaxyproject/galaxy/commit/f10047c4d31ef44ca6be03894224… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M templates/webapps/galaxy/admin/center.mako M templates/webapps/galaxy/admin/index.mako Log Message: ----------- Merge pull request #877 from dannon/minor_naming_tweak Slight tweak to sidebar section naming from 'security' to 'user manag… Compare: https://github.com/galaxyproject/galaxy/compare/77307e686b31...f10047c4d31e

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[galaxyproject/galaxy] c95955: Remove unused variable
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c95955e79e3c9dedb36b75734a859842a1c1dbed https://github.com/galaxyproject/galaxy/commit/c95955e79e3c9dedb36b75734a85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Remove unused variable Commit: e62b7e16950efd4aa798683f1b1909e3fdc37308 https://github.com/galaxyproject/galaxy/commit/e62b7e16950efd4aa798683f1b19… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Reinsert update state Commit: f6bfe8f7d0a00ea62e81cc1a1571ad40b5db0a2f https://github.com/galaxyproject/galaxy/commit/f6bfe8f7d0a00ea62e81cc1a1571… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Remove upload dataset handling Commit: 77307e686b31b2e300669f874b580d89be0e7fee https://github.com/galaxyproject/galaxy/commit/77307e686b31b2e300669f874b58… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #876 from guerler/tool_execution_002 Reinsert update state function to fix workflow execution which still relies on it. Compare: https://github.com/galaxyproject/galaxy/compare/60f6dc178580...77307e686b31

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[galaxyproject/galaxy] 7db17b: Refactor the remote user middleware for complexity
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7db17bb9a836d33a8dcb5a67febba0cbe4d3319c https://github.com/galaxyproject/galaxy/commit/7db17bb9a836d33a8dcb5a67febb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Refactor the remote user middleware for complexity Commit: cf7d10b3b55a979e7f6abe69059a660eac253b74 https://github.com/galaxyproject/galaxy/commit/cf7d10b3b55a979e7f6abe69059a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Correct typo Commit: 60f6dc1785802d307a0ac0e6c3bb33ca0b3fc161 https://github.com/galaxyproject/galaxy/commit/60f6dc1785802d307a0ac0e6c3bb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #875 from erasche/remoteuser-middleware-cleanup Refactor the remote user middleware for complexity Compare: https://github.com/galaxyproject/galaxy/compare/a937e233acb1...60f6dc178580

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[galaxyproject/galaxy] 470540: Expose all API keys to admins under REMOTE_USER
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 4705409d386f6cabe1874ac044617d6ed226a80e https://github.com/galaxyproject/galaxy/commit/4705409d386f6cabe1874ac04461… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a0ad2b75c29eca2c33ccfcdd4aa4a834c06c5265 https://github.com/galaxyproject/galaxy/commit/a0ad2b75c29eca2c33ccfcdd4aa4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #873 from erasche/api-key-backpatch [release_15.10] Expose all API keys to admins under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/69cd5a98dcda...a0ad2b75c29e

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[galaxyproject/galaxy] 90fca4: Expose all API keys to admins under REMOTE_USER
by GitHub 08 Oct '15

08 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 90fca4f47d762744b88923ff7404157f7027d235 https://github.com/galaxyproject/galaxy/commit/90fca4f47d762744b88923ff7404… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Expose all API keys to admins under REMOTE_USER This is the default setting for non-remote-user setups, this commit adjusts the middleware to behave as expected. Issue raised in http://dev.list.galaxyproject.org/User-API-keys-with-External-LDAP-authenti… Commit: a937e233acb14a9b15164e7602df85d5c77b2570 https://github.com/galaxyproject/galaxy/commit/a937e233acb14a9b15164e7602df… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-10-08 (Thu, 08 Oct 2015) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #872 from erasche/api-key-fix Expose API keys to admins under REMOTE_USER Compare: https://github.com/galaxyproject/galaxy/compare/5b93a66fae52...a937e233acb1

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[galaxyproject/galaxy] 5b93a6: Added missing lib/main.js
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5b93a66fae521726dffb9fb4712a07dfb14788ad https://github.com/galaxyproject/galaxy/commit/5b93a66fae521726dffb9fb4712a… Author: Nitesh Turaga <nitesh.turaga(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M doc/source/admin/interactive_environments.rst Log Message: ----------- Added missing lib/main.js

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[galaxyproject/galaxy] 47b34e: Verbosity is superfluous.
by GitHub 07 Oct '15

07 Oct '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47b34e844f174406eb3092e20bb89ff73d072da7 https://github.com/galaxyproject/galaxy/commit/47b34e844f174406eb3092e20bb8… Author: Dave B <dave(a)bx.psu.edu> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Verbosity is superfluous. Commit: add784a3e91104835bf769768ab09d47113deb5f https://github.com/galaxyproject/galaxy/commit/add784a3e91104835bf769768ab0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-10-07 (Wed, 07 Oct 2015) Changed paths: M test/docker/base/Dockerfile Log Message: ----------- Merge pull request #867 from davebx/docker Verbosity is superfluous. Compare: https://github.com/galaxyproject/galaxy/compare/cd9c13ab495f...add784a3e911

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