Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e85... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f68598... Author: Greg Von Kuster <ghv2@psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b08... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Commit: a5b7e6cb8e90387a7b9f6acb79b80a2114fa3928 https://github.com/galaxyproject/galaxy/commit/a5b7e6cb8e90387a7b9f6acb79b80... Author: Eric Enns <eric.enns@phac-aspc.gc.ca> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Updated tool input collection to only add items from a collection which are being used by the tool and not the entire collection. (Thanks to @markiskander for helping me find this). Commit: ee5a87af2e3d0a76da5df398826478bc4854c599 https://github.com/galaxyproject/galaxy/commit/ee5a87af2e3d0a76da5df39882647... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix for updating tool parameter dicts when a new parameter has been added to a section. Fixes issues seen during rerun under mentioned condition. Commit: d83e8d358f1b04683fa20245a66f12a8d881be4e https://github.com/galaxyproject/galaxy/commit/d83e8d358f1b04683fa20245a66f1... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1215 from blankenberg/rerunfix_15.10 [15.10] Fix for updating tool parameter dicts when a new parameter has been added to a section Commit: c9abc2bc97dbdbe85c82946ca1138a6f6139bb33 https://github.com/galaxyproject/galaxy/commit/c9abc2bc97dbdbe85c82946ca1138... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Fix for test/tool_shed/functional/test_1440_missing_env_sh_files.py . Properly order the installation of the repositories adding prior_installation_required="True". Otherwise filter_1440 is installed first and ends in INSTALLED status because of the logic of Repository.create_tool_dependency_with_initialized_env_sh_file() method contained in lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . Commit: 2b697e3c1ae76e4c718ed558e88a3c387d6e35c9 https://github.com/galaxyproject/galaxy/commit/2b697e3c1ae76e4c718ed558e88a3... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py Log Message: ----------- Fix detection of missing repository dependencies when reinstalling an updated Tool Shed repository. Fix test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py . Commit: d1684e7c9d9dc42918004dc15bf1e7d039c96088 https://github.com/galaxyproject/galaxy/commit/d1684e7c9d9dc42918004dc15bf1e... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #1224 from jmchilton/collection_naming_performance [15.10] Backport #1217 Commit: 516b079ab97d7fc0a40255d03dcaf2cb600a2384 https://github.com/galaxyproject/galaxy/commit/516b079ab97d7fc0a40255d03dcaf... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge pull request #1222 from nsoranzo/release_15.10_tool_shed_fixes [15.10] Tool Shed fixes. Commit: 11c46f4f35f3c1cb579198d28402ebacd51e6ec8 https://github.com/galaxyproject/galaxy/commit/11c46f4f35f3c1cb579198d28402e... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2015-12-04 (Fri, 04 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M test/tool_shed/test_data/1440_files/complex_dependency/tool_dependencies.xml Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e76933b55749...11c46f4f35f3