Documentation for dependency resolvers #1296
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* Add documentation on dependency resolvers
| @@ -1,7 +1,10 @@ | |||
| <dependency_resolvers> | |||
| <!-- the default configuration, first look for dependencies installed from the toolshed --> | |||
| <tool_shed_packages /> | |||
| <!-- then look for env.sh files profile according to the "galaxy packages" schema --> | |||
| <!-- then look for env.sh files in directories according to the "galaxy packages" schema. | |||
| These resolvers can take a base_path attribute to specify where to look for | |||
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I can't find the code where base_path attribute should be parsed, lib/galaxy/tools/deps/__init__.py seems to always use config.tool_dependency_dir .
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Its used in lib/galaxy/tools/deps/resolvers/resolver_mixins.py in the UsesToolDependencyDirMixin which is used by the galaxy_packages resolver.
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Thanks @pvanheus, nice work! |
* Use modulepath in both environment modules resolvers * Export MODULEPATH in generated shell command * Add logging for operation of dependency resolvers
* Replace {} and .format with %s and % to preserve Python 2.6 compatibility
* Add a modulepath= paranter to the fake resolver (Bunch object) used to test the modules dependency resolver
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Utterly and wonderfully fantastic @pvanheus! |
jmchilton
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Dec 11, 2015
Documentation for dependency resolvers
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Documentation largely derived from my blog post (http://pvh.wp.sanbi.ac.za/2015/10/09/how-galaxy-resolves-dependencies-or-not/) on how dependency resolvers are and can be configured for Galaxy.