Maintenance - Mise à jour mensuelle Lundi 6 Avril 2020 entre 7h00 et 9h00

Commit 88ba9f57 authored by Penom Nom's avatar Penom Nom

analysis update

parent f7249872
......@@ -68,21 +68,26 @@
<li><a href="#what" class="active">What is an Analysis</a></li>
<li><a href="#analysis-architecture" >Where to add a new Analysis</a></li>
<li><a href="#analysis" >The Analysis class</a></li>
<li><a href="#define_parameters">Define parameters</a>
<li><a href="#define_parameters">Analaysis.define_parameters</a>
<ul class="nav nav-stacked">
<li><a href="#parameters">Parameters</a></li>
<li><a href="#input_parameters">Inputs</a></li>
<li><a href="#output_parameters">Outputs</a></li>
</ul>
</li>
<li><a href="#define_analysis">Define analysis</a></li>
<li><a href="#process">Process</a>
<li><a href="#define_analysis">Analaysis.define_analysis</a>
<ul class="nav nav-stacked">
<li><a href="#define_analysis_fn">define_analysis</a></li>
<li><a href="#get_version_fn">get_version</a></li>
</ul>
</li>
<li><a href="#process">Analaysis.process</a>
<ul class="nav nav-stacked">
<li><a href="#functions">Functions</a></li>
<li><a href="#abstractions">Abstractions</a></li>
</ul>
</li>
<li><a href="#post_process">Post process</a></li>
<li><a href="#post_process">Analaysis.post_process</a></li>
<li><a href="#analysis_template">The analysis template</a></li>
</ul>
</nav>
......@@ -1013,24 +1018,8 @@ self.casava_directory.get_files( *args)</code></pre>
Those methods allow to presents the analysis to the user in the web interface.
</p>
<h2>get_version()</h2>
<p>The get version must return a string representing the version of this analysis.</p>
<h3>Example</h3>
<p>This example presents the get version of the fastqc analysis</p>
<pre class="pre-hl "><code class="python">def get_version(self):
cmd = [self.get_exec_path("fastqc"), "--version"]
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
stdout, stderr = p.communicate()
return stdout.split()[1]</code></pre>
<h3>Options</h3>
<p>No options for this</p>
<h2>define_analysis()</h2>
<div id="define_analysis_fn" class="subgroup">
<h2>define_analysis()</h2>
<p>
This method is in charge of describing the analysis. The name, description, options and so on.
</p>
......@@ -1080,10 +1069,31 @@ self.casava_directory.get_files( *args)</code></pre>
</tbody>
</table>
</div>
</div>
<div id="get_version_fn" class="subgroup">
<h2>get_version()</h2>
<p>The get version must return a string representing the version of this analysis.</p>
<h3>Example</h3>
<p>This example presents the get version of the fastqc analysis</p>
<pre class="pre-hl "><code class="python">def get_version(self):
cmd = [self.get_exec_path("fastqc"), "--version"]
p = Popen(cmd, stdout=PIPE, stderr=PIPE)
stdout, stderr = p.communicate()
return stdout.split()[1]</code></pre>
<h3>Options</h3>
<p>No options for this</p>
</div>
</section>
<section id="process" class="group">
<h1 class="page-header">Process</h1>
<h1 class="page-header">Analaysis.process</h1>
<p>The <code>process()</code> method is in charge of the specification of the executables used to process the data (a command
line or a Python function) and of the definition of the pattern of execution that determine how the functions are applied on the
data, what is named hereunder an abstraction. To build the process, ng6 provides two main functions named
......@@ -1459,7 +1469,7 @@ fastq2fasta.py --input splC.fastq --fasta splC.fasta --qual splC.qual</code></pr
<section id="post_process" class="group">
<h1 class="page-header">Post process</h1>
<h1 class="page-header">Analaysis.post_process</h1>
<p>
The <code>post_process()</code> method is executed after all the processing done in the analysis are done and just when the analysis is added in the database.
It waits for all output files to be available. In this method the developper can parse those output files and update the database with data to be presented
......
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