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<title>Uninstalling organisms from your RSAT instance</title>
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<h1 class="title toc-ignore">Uninstalling organisms from your RSAT instance</h1>
<h4 class="author"><em>Jacques van Helden</em></h4>
<h4 class="date"><em>2018-08-06</em></h4>
</div>
<div id="uninstalling-organisms-from-rsat" class="section level1">
<h1><span class="header-section-number">1</span> Uninstalling organisms from RSAT</h1>
<p>Let us imagine that we don’t need an organism anymore nd we want to suppress it from the list of available organisms on our RSAT server.</p>
<p>A concrete case: in the tutorial “<a href="install_organisms_from_ensembl.html">Installing genomes from Ensembl and EnsemblGenomes</a>” we installed <em>Saccharomyces cerevisiae</em> for the sake of test. After that, we installed the human genome, and since everything worked fine we would now like to suppress the version of <em>Saccharomyces cerevisiaie</em> downloaded from Ensembl.</p>
<p>We first need to identify the particular version that we installed from Ensembl.</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co">## Identify the full name of the Saccharomyces cerevisiae genome </span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co">## that was downloaded from Ensembl</span></a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="ex">supported-organisms</span> -source ensembl -taxon Saccharomyces</a>
<a class="sourceLine" id="cb1-4" data-line-number="4"><span class="co"># result (2018-08-06): Saccharomyces_cerevisiae_R64-1-1</span></a>
<a class="sourceLine" id="cb1-5" data-line-number="5"></a>
<a class="sourceLine" id="cb1-6" data-line-number="6"><span class="co">## Disable the usage of this genome (without deleting the files)</span></a>
<a class="sourceLine" id="cb1-7" data-line-number="7"><span class="ex">install-organism</span> -org Saccharomyces_cerevisiae_R64-1-1 -task uninstall</a>
<a class="sourceLine" id="cb1-8" data-line-number="8"></a>
<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co">## Check that this organism is not supported anymore</span></a>
<a class="sourceLine" id="cb1-10" data-line-number="10"><span class="ex">supported-organisms</span> -source ensembl -taxon Saccharomyces</a>
<a class="sourceLine" id="cb1-11" data-line-number="11"><span class="co">## Gives no result</span></a>
<a class="sourceLine" id="cb1-12" data-line-number="12"></a>
<a class="sourceLine" id="cb1-13" data-line-number="13"><span class="co">## Check if the genome data is still there in the RSAT genome folder.</span></a>
<a class="sourceLine" id="cb1-14" data-line-number="14"><span class="fu">du</span> -sm <span class="va">$RSAT</span>/public_html/data/genomes/Saccharomyces_cerevisiae_R64-1-1</a>
<a class="sourceLine" id="cb1-15" data-line-number="15"><span class="co">## Result: the folder is still there and occupies 39Mb</span></a>
<a class="sourceLine" id="cb1-16" data-line-number="16"></a>
<a class="sourceLine" id="cb1-17" data-line-number="17"><span class="co">## Erase the genome data </span></a>
<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="ex">install-organism</span> -org Saccharomyces_cerevisiae_R64-1-1 -task erase</a>
<a class="sourceLine" id="cb1-19" data-line-number="19"></a>
<a class="sourceLine" id="cb1-20" data-line-number="20"><span class="co">## Check if the genome data has well been removed now</span></a>
<a class="sourceLine" id="cb1-21" data-line-number="21"><span class="fu">du</span> -sm <span class="va">$RSAT</span>/public_html/data/genomes/Saccharomyces_cerevisiae_R64-1-1</a>
<a class="sourceLine" id="cb1-22" data-line-number="22"><span class="co">## Result: "No such file or directory"</span></a></code></pre></div>
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