Run one specific tool via Docker

Change according to your run (see How to change your file)

If you have already built the image with <tool>:<tag> (see the docker setup) you can run the following command to run the image and start the tool:

docker run -v <your mounted folder>:/MOUNT --user $(id -u):$(id -g) <tool>:<tag>

# Examples:
# If you are using our directory structure for your input and are in the dockers directory:
# Add the --rm flag to remove container, after run.

docker run -v $(pwd):/MOUNT --user $(id -u):$(id -g) --rm gsnap:0.1


  • Check Snakemake Output to see which rule failed.

  • if the rule that failed was named after a tool, check log files under output/<tool>-output/logs/ to see where the error was.