Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8ef1e51a4a06a74e2eaa9cd188a7f9194d345c27 https://github.com/galaxyproject/galaxy/commit/8ef1e51a4a06a74e2eaa9cd188a7f... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Remove `requirement` from shell_commands() parameters Commit: 11a9abbb2d7276208beed66bd153ba0fe7881d2b https://github.com/galaxyproject/galaxy/commit/11a9abbb2d7276208beed66bd153b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Return an OrderedSet of dependencies instead of a list This avoids activating mulled dependencies multiple times and fixes https://github.com/galaxyproject/galaxy/issues/4821. We use OrderedSet because the order of activation may matter for toolshed dependencies. Commit: 83eefb6b0413b764ef86f755fee65f80d1988170 https://github.com/galaxyproject/galaxy/commit/83eefb6b0413b764ef86f755fee65... Author: John Chilton <jmchilton@gmail.com> Date: 2017-11-06 (Mon, 06 Nov 2017) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/lmod.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/resolver_mixins.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #4945 from nsoranzo/refactor_shell_commands Activate mulled dependencies once per job Compare: https://github.com/galaxyproject/galaxy/compare/363a2e063681...83eefb6b0413