Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: b01d20b1be9e1cf579a3c2bd42a3d524548d2240 https://github.com/galaxyproject/galaxy/commit/b01d20b1be9e1cf579a3c2bd42a3d... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Fix for server error when installing some repos. Examples: IUC's gatk2 repository, devteam's samtools_rmdup. When attempting to install either of those, or another repository that has tool tests with an input parameter that does not have a value attribute, the repository would be stuck in state 'Cloning' and show a debug link in the log. This commit resolves that error. Commit: 19c85e070534f4318cca3e728c52c91a27163f4a https://github.com/galaxyproject/galaxy/commit/19c85e070534f4318cca3e728c52c... Author: Jeremy Goecks <jgoecks@gwu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/viz/sweepster.js M static/maps/mvc/tools.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/viz/sweepster.js Log Message: ----------- Fixes to make Sweepster work again: (a) update template syntax to match changes made in underscore v1.7 and (b) update tool rerun to account for API changes. Commit: 04a5bd78f021968ccd1b98eec2968ecdc3c93f77 https://github.com/galaxyproject/galaxy/commit/04a5bd78f021968ccd1b98eec2968... Author: nitesh1989 <nitesh.turaga@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Fix: rdata extension type Commit: a1cc1ed94bba19bcc131f41d6cfc80fe1ca03009 https://github.com/galaxyproject/galaxy/commit/a1cc1ed94bba19bcc131f41d6cfc8... Author: nitesh1989 <nitesh.turaga@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix: Typo the other way. Supposed to be "RData" Ref: https://stat.ethz.ch/R-manual/R-devel/library/base/html/save.html Commit: ac43237e49e8660b1812f8662d081d4b0d3bf3de https://github.com/galaxyproject/galaxy/commit/ac43237e49e8660b1812f8662d081... Author: Daniel Blankenberg <dan.blankenberg@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/tool_shed/util/web_util.py Log Message: ----------- Fix for toolshed escape method, where an error/log message contains non-ASCII characters. Commit: d2e61e8af4c933b733c640f46f831bf424bc0197 https://github.com/galaxyproject/galaxy/commit/d2e61e8af4c933b733c640f46f831... Author: guerler <aysam.guerler@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-library.js M static/maps/mvc/ui/ui-select-library.js.map M static/scripts/mvc/ui/ui-select-library.js Log Message: ----------- Filter deleted library datasets Commit: 8d96580fc20e2a6322fdacb1b25635fb4573c934 https://github.com/galaxyproject/galaxy/commit/8d96580fc20e2a6322fdacb1b2563... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Correct examples in workflow invocations. Commit: 51991f03caf3b1ed15d4672160cf0f50e6e537db https://github.com/galaxyproject/galaxy/commit/51991f03caf3b1ed15d4672160cf0... Author: Dave B <dave@bx.psu.edu> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: R templates/webapps/tool_shed/message.mako Log Message: ----------- Stop creating database/message.mako.py Commit: 64edf4e2f953f21e4e52c6647a65960c6c44945a https://github.com/galaxyproject/galaxy/commit/64edf4e2f953f21e4e52c6647a659... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M templates/webapps/reports/base_panels.mako Log Message: ----------- fix the class for reports brand so it is actually shown and not black text on dark background Commit: 4fcdf9fda1d21ec5669daa8e9a4e3e84171bb617 https://github.com/galaxyproject/galaxy/commit/4fcdf9fda1d21ec5669daa8e9a4e3... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-27 (Thu, 27 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/tools.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/viz/sweepster.js M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/util/web_util.py M static/maps/mvc/tools.js.map M static/maps/mvc/ui/ui-select-library.js.map M static/maps/viz/sweepster.js.map M static/scripts/mvc/tools.js M static/scripts/mvc/ui/ui-select-library.js M static/scripts/viz/sweepster.js M templates/webapps/reports/base_panels.mako R templates/webapps/tool_shed/message.mako Log Message: ----------- Merge pull request #657 from jmchilton/dev_1507_backports [15.07] Backport various dev fixes. Compare: https://github.com/galaxyproject/galaxy/compare/71125326f842...4fcdf9fda1d2