Running tophat dockerfile in background
Assuming your user is in the group permitted to use docker:

docker pull quay.io/biocontainers/tophat:2.1.1--py27_3
nohup docker run -v /some/path:/data quay.io/biocontainers/tophat:2.1.1--py27_3 tophat2 ... &amp;


The only thing to remember is to mount everything you'll need into the docker container (/data in the example above). If you need to debug things then you can add the -it flag to docker run and use bash as the command.

As an aside, you might find using screen or tmux preferable to nohup ... &amp;, since you can reconnect to sessions with them.