add resources section help

docs/jflow-advanced-configuration.html

@@ -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">

docs/jflow-core-component.html

@@ -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">

docs/jflow-core-workflow.html

@@ -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>