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README.Dockerfile.md

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OxoG filter

A dockerfile based on broadinstitute/pcawg_public (created by Gordon Saksena). This dockerfile has the following changes:

  • It contains a script run_oxog_tool.py that is used to run the OxoG filter inside the container. This script is based on the python_cmd found in https://github.com/broadinstitute/pcawg_public/blob/master/taskdef.pcawg_oxog.wdl
  • It contains gosu, so that it can run certain programs as root, to get around some cwltool restrictions.
  • It declares the paths /opt and /root/.python-eggs as docker volumes to make them readable, to get around some cwltool restrictions on read-only filesystems.