RAPPEL : Opération de maintenance > ForgeMIA indisponible le 20 Janvier entre 7h et 12h

Commit adc05238 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

add resources section help

parent c265656a
......@@ -67,9 +67,9 @@
<!--Nav Bar -->
<nav class="col-xs-3 bs-docs-sidebar">
<ul id="sidebar" class="nav nav-stacked fixed">
<li><a href="#email" class="active">Email</a></li>
<li><a href="#ressources">Ressources</a></li>
<li><a href="#components">Components</a></li>
<li><a href="#email" class="active">Email section</a></li>
<li><a href="#ressources">Ressources section</a></li>
<li><a href="#components">Components section</a></li>
<li><a href="#more">More configuration</a></li>
</ul>
</nav>
......@@ -104,14 +104,14 @@ from_password =
<section id="ressources">
<h1 class="page-header">Ressources <small>section</small></h1>
<p>It can be usefull to You must edit the <code>application.properties</code> file to configure the application.
Here under the required parameters, for advanced configuration please see
<a href="./jflow-advanced-configuration.html">this page</a>...</p>
<p>In a production environment, it can be useful to set an ensemble of variables, such as path to databanks, for
multiple workflows. Thus, jflow gives access to ressources settled within the <code>application.properties</code> file.
All the values settled within this section are then accessible from any <code>Component</code> or <code>Workflow</code>
through the <code>get_resource()</code> class method.</p>
<pre class="pre-hl "><code class="ini">[resources]
typo3_src = http://prdownloads.sourceforge.net/typo3/typo3_src+dummy-4.7.12.zip
#phix_bwa = /bank/bwadb/phi.fa
#ecoli_bwa = /bank/bwadb/ecoli536
#yeast_bwa = /bank/bwadb/yeast.nt</code></pre>
ecoli_db = /path/to/ecoli536
phix_db = /path/to/phi.fa
...</code></pre>
</section>
<section id="components">
......
......@@ -87,6 +87,7 @@
<ul class="nav nav-stacked">
<li><a href="#pre_process">Pre process</a></li>
<li><a href="#post_process">Post process</a></li>
<li><a href="#get_resource">Get Resource</a></li>
</ul>
</li>
<li><a href="#external_components" >External components</a></li>
......@@ -1233,6 +1234,35 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
<p><code>post_process()</code> is executed right after the <code>process</code> method and cannot be used to call a <code>ShellFunction</code> or a
<code>PythonFunction</code>. This method can be useful to perform some database transactions and to synchronize data.</p>
</div>
<div id="get_resource" class="subgroup">
<h2>Get shared resources</h2>
<p>The method <code>get_resource()</code>, giving a specific resource, returns the defined value within the <code>resource</code>
section of the jflow configuration file.</p>
<h3>Options</h3>
<p>There is one required argument : resource.</p>
<div class="table-responsive">
<table class="table table-bordered table-striped">
<thead>
<tr>
<th>Name</th>
<th>Type</th>
<th>Required</th>
<th>Default value</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>resource</td>
<td>string</td>
<td>true</td>
<td>None</td>
<td>The resource name for which is requested the configured value.</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
<section id="external_components" class="group">
......
......@@ -86,6 +86,7 @@
<li><a href="#set_to_address">Set to address</a></li>
<li><a href="#set_subject">Set subject</a></li>
<li><a href="#set_message">Set message</a></li>
<li><a href="#get_resource">Get resource</a></li>
</ul>
</li>
</ul>
......@@ -762,6 +763,35 @@ bwamem = self.add_component("BWAmem", [bwaindex.databank, self.reads])</code></p
</table>
</div>
</div>
<div id="get_resource" class="subgroup">
<h2>Get shared resources</h2>
<p>The method <code>get_resource()</code>, giving a specific resource, returns the defined value within the <code>resource</code>
section of the jflow configuration file.</p>
<h3>Options</h3>
<p>There is one required argument : resource.</p>
<div class="table-responsive">
<table class="table table-bordered table-striped">
<thead>
<tr>
<th>Name</th>
<th>Type</th>
<th>Required</th>
<th>Default value</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>resource</td>
<td>string</td>
<td>true</td>
<td>None</td>
<td>The resource name for which is requested the configured value.</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
</div>
</div>
......
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