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Fix Conda and BioContainers functionality for CWL tool development. #828

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merged 3 commits into from May 17, 2018

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jmchilton commented May 16, 2018

  • Bring in galaxy-lib update to parse CWL SoftwareRequirements into Galaxy requirements. This fixes conda_install and conda_env commands for instance and enables the next change.
  • Annotate conda and biocontainers linters as checking CWL files - enables support for planemo lint --conda_requirements, planemo lint --biocontainers on CWL tools.
  • If --no-container is specified when using the "cwltool" engine for the test or run command, turn on Planemo's default dependency resolvers for the cwltool run. The can be combined with --no_dependency_resolution to turn off dependency resolution the same as Galaxy - this is close to what the previous behavior of cwltool in Planemo was.
  • If --biocontainers is specified as an argument to Planemo during test or run commands - turn them on for cwltool as well (using its --beta-use-biocontainers command).

jmchilton added some commits May 16, 2018

Fix CWL support to handle SoftwareRequirements as Galaxy requirements.
Should enable support "planemo lint --conda_requirements", "planemo lint --biocontainers", "planemo conda_install", "planemo conda_env".
Fix dependency resolvers and --biocontainers to work with cwltool.
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).

@jmchilton jmchilton force-pushed the jmchilton:cwl_fixes_6 branch 2 times, most recently from a82de39 to 66f2c7c May 16, 2018

Rev cwltool for a Python 3 fix.
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.

@jmchilton jmchilton force-pushed the jmchilton:cwl_fixes_6 branch from 66f2c7c to 7add211 May 17, 2018

@jmchilton jmchilton merged commit 6de6214 into galaxyproject:master May 17, 2018

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