I am trying to run fmriprep on an HTCondor system, using the Docker container.
To submit the job, I specify that the
universe = docker and that the docker_image is
poldracklab/fmriprep:latest. This successfully pulls and then loads the docker image.
However, since I am effectively trying to run the script from “within” the Docker image (since it’s loaded as the universe), I can’t figure out how to go from:
docker run -ti --rm -v filepath/to/data/dir:/data:ro -v filepath/to/output/dir:/out \ poldracklab/fmriprep:latest /data /out/out participant
to a command that can be run without first invoking
docker (since I’m already in it).
fmriprep-docker /path/to/data/dir /path/to/output/dir participant doesn’t work because it too invokes docker first).
So: how does one go from the command invoking docker to a command run within the docker image?