<p>We are trying to run Snakemake workflows on Kubernetes on premise infrastructure. We are using OpenShift OKD on a MapR filesystem more precisely.</p>

<p>We followed the <a href="https://snakemake.readthedocs.io/en/stable/executable.html#executing-a-snakemake-workflow-via-kubernetes" rel="nofollow noreferrer">official documentation</a> command:</p>

<pre><code>snakemake --kubernetes --use-conda --default-remote-provider $REMOTE --default-remote-prefix $PREFIX
</code></pre>

<p>But the command line help provided for <code>--default-remote-provider</code> and <code>--default-remote-prefix</code> are not clear about how we should execute Snakemake pipelines on a on premise Kubernetes or OpenShift cluster:</p>

<pre><code>--default-remote-provider: choose from 'S3', 'GS', 'FTP', 'SFTP', 'S3Mocked', 'gfal', 'gridftp', 'iRODS'
</code></pre>

<p>Also, the official documentation states:</p>

<blockquote>
  <p>In this mode, Snakemake will assume all input and output files to be stored in a given remote location, configured by setting $REMOTE to your provider of choice (e.g. GS for Google cloud storage or S3 for Amazon S3) and $PREFIX to a bucket name or subfolder within that remote storage.</p>
</blockquote>

<p>So I was wondering:</p>

<ul>
<li><p>How does one should proceed to deploy Snakemake workflow to on premise OpenShift/Kubernetes installation? </p></li>
<li><p>Is there example (such as github repo or blog) of running Snakemake on premise clusters?</p></li>
<li><p>In particular, I am not sure which remote provider should be chosen, and how to provide the prefix (can it be linked to a Kubernetes Persistent Volume Claim?)</p></li>
</ul>

<p>Thanks a lot for your help!</p>

vemonet
<p>Not really familiar with on premise Kubernetes set up, but <a href="https://snakemake.readthedocs.io/en/stable/executing/cloud.html" rel="nofollow noreferrer">this segment of snakemake's documentation on cluster execution may help.</a></p>
<p>The portion you've highlighted relates more to cloud implementation of compute clusters.</p>
