text: user7209: 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?
  
  user77: 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 screen or tmux preferable to nohup ... &, since you can reconnect to sessions with them.
  
original_text: 7209: <p>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 &amp; to run tophat2 through docker, if I need some user interaction?</p>
   77: <p>Assuming your user is in the group permitted to use docker:</p>
  
  <pre><code>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;
  </code></pre>
  
  <p>The only thing to remember is to mount everything you'll need into the docker container (<code>/data</code> in the example above). If you need to debug things then you can add the <code>-it</code> flag to <code>docker run</code> and use <code>bash</code> as the command.</p>
  
  <p>As an aside, you might find using <code>screen</code> or <code>tmux</code> preferable to <code>nohup ... &amp;</code>, since you can reconnect to sessions with them.</p>
  