Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 946d64b8f7dc08b92ebb03f34a91cab8aa7ecfbb https://github.com/galaxyproject/galaxy/commit/946d64b8f7dc08b92ebb03f34a91c... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- LMOD Dependency resolver - Initial commit (lib lmod.py) Initial commit of a prototype dependency resolver based on the LMOD environment modules system. Commit: 4d143479d5998531cc4803af11579e12d160c87b https://github.com/galaxyproject/galaxy/commit/4d143479d5998531cc4803af11579... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- Update of the dependency_resolvers_conf.xml.sample file Addition of the LMOD Dependency resolver to the appropriate sample configuration file (dependency_resolvers_conf.xml.sample). Comment lines have also been added to describe the possible attributes of the resolver as well as their default values. Commit: e84284c477182b3c03e785b79f93dd88d63e6ebd https://github.com/galaxyproject/galaxy/commit/e84284c477182b3c03e785b79f93d... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- LMOD Dependency resolver - Default mapping file If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules. Commit: fed3206a87e4ae4ede380c90cfa3409220847cf7 https://github.com/galaxyproject/galaxy/commit/fed3206a87e4ae4ede380c90cfa34... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Fix errors reported by the initial Travis tests Fix incorrect numbers of blank lines. Fix deprecated syntax. Commit: 09887529765ba88adb70e739d1b9d8896cb86229 https://github.com/galaxyproject/galaxy/commit/09887529765ba88adb70e739d1b9d... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Syntax fix in the shell_commands method The built command now reflect more directly the command that is really executed by the the LMOD "module" bash function when a user execute "module load package_name/package_version". Commit: 574e697a4d66a53f298f37f4987d31db96ff8e14 https://github.com/galaxyproject/galaxy/commit/574e697a4d66a53f298f37f4987d3... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample Log Message: ----------- Dependency_resolvers_conf.xml - More explanations Some more explanations about the versionless mode have been added. Commit: db5efdaa7cbc197eaf6a777d4d390de24b212e88 https://github.com/galaxyproject/galaxy/commit/db5efdaa7cbc197eaf6a777d4d390... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/lmod.py Log Message: ----------- Clearer comment lines in the has_module method A comment of the has_module method of the AvailModuleChecker class has been modified to be clearer and more explicit. Commit: eda36ffb99a1abec8f878c0b7ae194938781c8d6 https://github.com/galaxyproject/galaxy/commit/eda36ffb99a1abec8f878c0b7ae19... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- LMOD Dependency resolver - Unit tests added The unit/tools/tests_tool_deps.py script has been updated to includ unit tests for the LMOD dependency resolver. Commit: bbec357bbd744b9e0d760e8d0903adfa43d1b7e2 https://github.com/galaxyproject/galaxy/commit/bbec357bbd744b9e0d760e8d0903a... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix the import order error raised by Travis The order of the import statements in the test_tool_deps script was incorrect (as stated by travis). That should no longer be the case. Commit: 9822f5f2a91fae7e3420a06c58f2621a2cf084ac https://github.com/galaxyproject/galaxy/commit/9822f5f2a91fae7e3420a06c58f26... Author: Aurélien Bernard <aurelien.bernard.bioinfo63@gmail.com> Date: 2017-08-24 (Thu, 24 Aug 2017) Changed paths: M test/unit/tools/test_tool_deps.py Log Message: ----------- Fix attempt for the modulepath issue in unit tests On a computer where LMOD is not installed, the MODULEPATH variable is not defined and the modulepath attributes of the LMOD dependency resolver must be used. Commit: 1e3bd2d4e831331b8e3b314bac287288fa4533fc https://github.com/galaxyproject/galaxy/commit/1e3bd2d4e831331b8e3b314bac287... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-05 (Tue, 05 Sep 2017) Changed paths: M config/dependency_resolvers_conf.xml.sample A config/lmod_modules_mapping.yml.sample A lib/galaxy/tools/deps/resolvers/lmod.py M test/unit/tools/test_tool_deps.py Log Message: ----------- Merge pull request #4489 from arbernard/LMOD_Dependency_resolver New Dependency resolver for the LMOD environment modules system Compare: https://github.com/galaxyproject/galaxy/compare/6e6845b4987a...1e3bd2d4e831