Fix Conda and BioContainers functionality for CWL tool development.#828
Merged
jmchilton merged 3 commits intogalaxyproject:masterfrom May 17, 2018
Merged
Fix Conda and BioContainers functionality for CWL tool development.#828jmchilton merged 3 commits intogalaxyproject:masterfrom
jmchilton merged 3 commits intogalaxyproject:masterfrom
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Should enable support "planemo lint --conda_requirements", "planemo lint --biocontainers", "planemo conda_install", "planemo conda_env".
By default, don't mess with cwltool's normal behavior to make it more like a Planemo configured Galaxy. However, if --no-container is specified go ahead and turn on Planemo's default dependency resolvers for the cwltool run. Also if --biocontainers is specified to Planemo - turn them on for cwltool as well (--beta-use-biocontainers).
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There was a Python 3 problem with the dependency resolver stuff in the version previously targetted, reving this and praying. Had to replace some CWL draft 3 testing artifacts with version 1.0 since the former is not longer compatible with latest versions of CWL.
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conda_installandconda_envcommands for instance and enables the next change.planemo lint --conda_requirements,planemo lint --biocontainerson CWL tools.--no-containeris specified when using the "cwltool" engine for thetestorruncommand, turn on Planemo's default dependency resolvers for the cwltool run. The can be combined with--no_dependency_resolutionto turn off dependency resolution the same as Galaxy - this is close to what the previous behavior of cwltool in Planemo was.--biocontainersis specified as an argument to Planemo duringtestorruncommands - turn them on for cwltool as well (using its--beta-use-biocontainerscommand).