Commit 46ee0a86 authored by Céline Noirot's avatar Céline Noirot
Browse files

Documentation for get_cpu and get_memory

parent 61a34f3e
......@@ -271,9 +271,20 @@ cutadapt = /path/to/cutadapt</code></pre>
<h1 class="page-header">Components <small>section</small></h1>
<p>In a production environment, it can be useful to custom DMS options for each components. To do so, within the <code>components</code>
section in the jflow configuration file, add a line following the schema: [component_name].batch_options = [options].</p>
<p>Cpu and memory values are then avalaible in the component via the methods <code>get_cpu()</code> and <code>get_memory()</code> on local and SGE enviroment only/</p>
<h3>Local configuration</h3>
<p>you can provide option with format <code>mem=XX[K|M|G] cpu=XX"</code></p>
<pre class="pre-hl "><code class="ini">[components]
BWAIndex.batch_options = "mem=1G"
BWAmem.batch_options = "mem=10G cpu=4"</code></pre>
<h3>SGE configuration</h3>
<p>you can provide option as you would provide to SGE</code></p>
<pre class="pre-hl "><code class="ini">[components]
BWAIndex.batch_options = -l mem=1G -l h_vmem=1G -q myflowq
BWAmem.batch_options = -l mem=10G -l h_vmem=10G -q myflow2q</code></pre>
</section>
<section id="workflows">
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......@@ -1266,6 +1266,18 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
</table>
</div>
</div>
<div id="get_cpu" class="subgroup">
<h2>Get cpu</h2>
<p><code>get_cpu()</code> return the cpu value of <code>batch_options</code> configuration for this component (available for <b>local and sge only</b>).
This option is usefull to set software parameter that needs more than one CPU.</p>
<p>For more information about how to configure a component see advanced configuration</p>
</div>
<div id="get_memory" class="subgroup">
<h2>Get memory</h2>
<p><code>get_memory()</code> return the memory value of <code>batch_options</code> configuration for this component (available for <b>local and sge only</b>).
This option is usefull to set software parameter that needs specific value of memory.</p>
<p>For more information about how to configure a component see advanced configuration</p>
</div>
</section>
<section id="external_components" class="group">
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