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Add initial working slurm/apptainer configuration and run script for JHU discovery. - #59

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acoffman wants to merge 1 commit into
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jhu-discovery-config
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acoffman wants to merge 1 commit into
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jhu-discovery-config

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This PR includes three files:

  • The Cromwell configuration we are currently using on DISCOVERY. It assumes a few things:

    • Images are already pulled and converted from Docker images to .SIF image files on a shared disk location
    • Image names are converted from org/image:version to org_image_version.sif to make them safe as filenames
    • The image cache path is hardcoded to /projects/beyond_binding/cromwell_immuno_test/shared-sif-images/ currently. I don't know if we'll want to make that parametrizable going forward.
  • A new version of runCromwellWDL.sh modified to handle the differences in the cluster environment from our compute1 or GCP environments.

  • A concrete example of the command I ran in order to get a successful run of immuno.wdl on the JHU cluster with the HCC1395 test data

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