<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>

CC BY-SA 4.0
2020-02-13T07:10:03.690Z
2020-02-13T07:10:03.690Z
Devon Ryan
<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>

CC BY-SA 4.0
2020-02-12T18:35:23.587Z
Do you have root access? Docker generally requires root (as it normally is systemctl service and hard/janky to use otherwise)... Does the server not have a queuing system? Or is this a classic furtive job in the login node of an oversubscribed cluster? Also if an admin may kill a nohup job, they may kill your docker job.
Matteo Ferla
<phylogenetics><bash><docker>
Running tophat dockerfile in background
# Running tophat dockerfile in background

(Asked by: username_0 on 2020-02-12)

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?

**Tags:** phylogenetics, bash, docker
> **Comments:**
> **username_1**: Do you have root access? Docker generally requires root (as it normally is systemctl service and hard/janky to use otherwise)... Does the server not have a queuing system? Or is this a classic furtive job in the login node of an oversubscribed cluster? Also if an admin may kill a nohup job, they may kill your docker job.  

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## 1 answers

### Answer by username_2 on 2020-02-13. Score: 2

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.


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