Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1429d4340f11591768bb853fd646508e32e0501 https://github.com/galaxyproject/galaxy/commit/b1429d4340f11591768bb853fd646... Author: John Chilton <jmchilton@gmail.com> Date: 2017-03-14 (Tue, 14 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Mirror latest galaxy-lib changes for Conda and CWL improvements. - I added more flexibility to mulled operations to work around bugs on OS X (galaxyproject/galaxy-lib#50). - I added the ability to use local packages with the Conda resolver (galaxyproject/galaxy-lib#47) - this allows Galaxy when used with Planemo to use locally built packages. Including Nicola's suggested changes here (https://github.com/galaxyproject/galaxy-lib/commit/6d53fc7dec6c48ea8fb00fa37...). - I switched the default Conda prefix to miniconda3 so the name matches what Galaxy is actually installing. galaxyproject/galaxy-lib#48. This would never actually be used with Galaxy since we decided it should maintain its own prefix rather than using the default - it is important for Planemo though. - I synced the galaxy.tools.cwl package with my latest downstream work that provides updates for latest developments in cwltool. https://github.com/galaxyproject/galaxy-lib/pull/53 - I added the ability to load tools via URI-like strings in addition to simple paths - this allows referencing URLs and Dockstore/GA4GH tools directly from the command-line with Planemo. https://github.com/galaxyproject/galaxy-lib/pull/52 There are some other bug fixes outside of these three main PRs related to the second point - minor refinements to get conda-build dependencies working and working automatically. - galaxyproject/galaxy-lib@bdacc4d - galaxyproject/galaxy-lib@1b7bca6 - galaxyproject/galaxy-lib@36b2e65 Commit: 031ce2307367f021646c2a1640112599320076fc https://github.com/galaxyproject/galaxy/commit/031ce2307367f021646c2a1640112... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-03-17 (Fri, 17 Mar 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/resolvers/conda.py A lib/galaxy/tools/fetcher.py M lib/galaxy/tools/loader_directory.py A lib/galaxy/tools/locations/__init__.py A lib/galaxy/tools/locations/dockstore.py A lib/galaxy/tools/locations/file.py A lib/galaxy/tools/locations/http.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py Log Message: ----------- Merge pull request #3742 from jmchilton/galaxy-lib-20170311 Mirror latest galaxy-lib changes for Conda and CWL improvements. Compare: https://github.com/galaxyproject/galaxy/compare/d50ca25a822a...031ce2307367