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<title>ARETE</title>
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<title>Citations - ARETE</title>
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<title>Roadmap - ARETE</title>
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65 changes: 51 additions & 14 deletions faq/index.html
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<title>FAQ - ARETE</title>
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<li class="toctree-l2"><a class="reference internal" href="#how-do-i-x">How do I x?</a>
<li class="toctree-l2"><a class="reference internal" href="#how-do-i-run-arete-in-a-slurm-hpc-environment">How do I run ARETE in a Slurm HPC environment?</a>
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<div class="section" itemprop="articleBody">

<h1 id="frequently-asked-questions">Frequently Asked Questions</h1>
<h2 id="how-do-i-x">How do I x?</h2>
<h2 id="how-do-i-run-arete-in-a-slurm-hpc-environment">How do I run ARETE in a Slurm HPC environment?</h2>
<ul>
<li>Set a config file under <code>~/.nextflow/config</code> to use the slurm executor:</li>
</ul>
<pre><code class="language-json"> process {
executor = 'slurm'
pollInterval = '60 sec'
submitRateLimit = '60/1min'
queueSize = 100
// If an account is necessary:
clusterOptions = '--account=&lt;my-account&gt;'
}
</code></pre>
<p>See the <a href="https://www.nextflow.io/docs/latest/config.html#scope-executor">Nextflow documentation</a> for a description of these options.</p>
<ul>
<li>Now, when running ARETE, you'll need to set additional options if your compute nodes don't have network access - as is common for most Slurm clusters. The example below uses the default test data, i.e. the <code>test</code> profile, for demonstration purposes only.</li>
</ul>
<pre><code class="language-bash">nextflow run beiko-lab/ARETE \
--db_cache path/to/db_cache \
--bakta_db path/to/baktadb \
-profile test,singularity
</code></pre>
<p>Apart from <code>-profile singularity</code>, which just makes ARETE use Singularity/Apptainer containers for running the tools, there are two additional parameters:</p>
<ul>
<li>
<p><code>--db_cache</code> should be the location for the pre-downloaded databases used in the DIAMOND alignments (i.e. Bacmet, VFDB, ICEberg2 and CAZy FASTA files) and in the Kraken2 taxonomic read classification.</p>
<ul>
<li>Although these tools run by default, you can change the selection of annotation tools by changing <code>--annotation_tools</code> and
skip Kraken2 by adding <code>--skip_kraken</code>. See the <a href="https://beiko-lab.github.io/arete/params/">parameter documentation</a> for a full list of parameters and their defaults.</li>
</ul>
</li>
<li>
<p><code>--bakta_db</code> should be the location of the pre-downloaded <a href="https://github.com/oschwengers/bakta#database-download">Bakta database</a></p>
<ul>
<li>Alternatively, you can use Prokka for annotating your assemblies, since it doesn't require a downloaded database (<code>--use_prokka</code>).</li>
</ul>
</li>
</ul>

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