I need to use tophat2 to align some sequences, and I wish to use the docker container. These are large sequences so it will take a long time, plus I'm working on a university server so the chances of being kicked off the server are very high. How can I use nohup and & to run tophat2 through docker, if I need some user interaction?
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 ... &
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
tmux preferable to
nohup ... &, since you can reconnect to sessions with them.