Run one specific tool via Docker
Change config.sh according to your run (see How to change your config.sh 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.