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

Commit c265656a authored by Jerome Mariette's avatar Jerome Mariette
Browse files

add email configuration help

parent 884bc84c
......@@ -14,6 +14,9 @@
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......@@ -64,10 +67,73 @@
<!--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="#more">More configuration</a></li>
</ul>
</nav>
<div class="col-xs-12 col-sm-9">
<div class="col-xs-12 col-sm-9">
<section id="email">
<h1 class="page-header">Email <small>section</small></h1>
<p>jflow offers the possibility to send emails to the users at the end of a workflow execution. This can be done
by editing the <code>email</code> section of the <code>application.properties</code> file.</p>
<p> To access this functionality, <code>smtp_server</code>, <code>smtp_port</code>, <code>from_address</code>
and <code>from_password</code> are required parameters. The values <code>to_address</code>, <code>subject</code>
and <code>message</code> can be globaly set from the jflow configuration file or can be set within a workflow by
using respectivly the <code>self.set_to_address()</code>, <code>self.set_subject()</code> and <code>self.set_message()</code>
methods. This allows to request, as a workflow input, a user email in order to send him a notification when the workflow
is over.
<pre class="pre-hl "><code class="ini">[email]
# if you want an email to be sent at the end of the workflow execution
# set the smtp_server and the from_address values
smtp_server =
smtp_port =
from_address =
from_password =
# uncomment and set if you want to use these values for all the workflow
# these variables can be overloaded within the workflow implementation by
# using self.set_to_address("address"), self.set_subject("subject"),
# self.set_message("message") functions
#to_address =
#subject =
#message =</code></pre>
</section>
<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>
<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>
</section>
<section id="components">
<h1 class="page-header">Components <small>section</small></h1>
<p>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>
<pre class="pre-hl "><code class="ini">[components]
#Bismark.batch_options = -pe parallel_smp 8 -q wflowq
#BismarkMethylationExtractor.batch_options = -l mem=8G -l h_vmem=16G -q wflowq
#BWA.batch_options = -q unlimitq
#AlignmentStats.batch_options = -q unlimitq
#ContaminationSearch.batch_options = -q unlimitq</code></pre>
</section>
<section id="more">
<h1 class="page-header">More <small>configuration</small></h1>
<p>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>
</section>
</div><!--/span-->
</div><!--/row-->
......@@ -89,6 +155,11 @@
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......@@ -83,6 +83,9 @@
<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="#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>
</ul>
</li>
</ul>
......@@ -674,6 +677,91 @@ bwamem = self.add_component("BWAmem", [bwaindex.databank, self.reads])</code></p
<p><code>post_process()</code> is executed right after the <code>process</code> method and cannot be used to add components. This method can
be useful to perform some database transactions and to synchronize data.</p>
</div>
<div id="set_to_address" class="subgroup">
<h2>Set to address</h2>
<p><code>set_to_address()</code> overwrite the value <code>to_address</code> defined in the jflow configuration file.</p>
<h3>Options</h3>
<p>There is one required argument : to_address.</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>to_address</td>
<td>string</td>
<td>true</td>
<td>None</td>
<td>The email address to use to send an email to the user once the workflow is completed.</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="set_subject" class="subgroup">
<h2>Set email subject</h2>
<p><code>set_subject()</code> </code> overwrite the value <code>subject</code> defined in the jflow configuration file.</p>
<h3>Options</h3>
<p>There is one required argument : subject.</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>subject</td>
<td>string</td>
<td>true</td>
<td>None</td>
<td>The email subject to use for the email sent to the user once the workflow is completed.</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="set_message" class="subgroup">
<h2>Set email message</h2>
<p><code>set_message()</code> overwrite the value <code>message</code> defined in the jflow configuration file.</p>
<h3>Options</h3>
<p>There is one required argument : message.</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>message</td>
<td>string</td>
<td>true</td>
<td>None</td>
<td>The email message to use for the email sent to the user once the workflow is completed.</td>
</tr>
</tbody>
</table>
</div>
</div>
</section>
</div>
</div>
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