Commit ebc4cde0 authored by Celine Noirot's avatar Celine Noirot

add link on detailed documentation

parent dd430e29
......@@ -114,7 +114,7 @@
<p>
The first thing to do before implementing the analyses and the NG6Workflow, is to create the folder tree.
A ng6workflow is a <code>Python package</code> defined by a folder with a <code>__init__.py</code> file.
A <a href="./core-workflow.html">ng6workflow</a> is a <code>Python package</code> defined by a folder with a <code>__init__.py</code> file.
</p>
<p>
Within NG6 sources, add a package named <code>quickstart</code> and within this package create an other package named <code>components</code> (with <code>__init__.py</code> inside)
......@@ -179,7 +179,7 @@
</ul>
<p>
The <code>Python</code> class must inherit <code>ng6.analysis.Analysis</code>. While writting the Analysis, several methods must be overloaded:
The <code>Python</code> class must inherit <code>ng6.analysis.Analysis</code>. While writting the <a href="./core-analysis.html">Analysis</a>, several methods must be overloaded:
</p>
<ul>
......@@ -247,7 +247,7 @@ class QIlluminaFilter (Analysis):
pattern='{basename_woext}.stdout', items=self.input_fastqs)</code></pre>
</div>
<p>Using those parameters definition will lead to this command structure:</p>
<p>Using those <a href="./core-analysis.html#define_parameters">parameters definition</a> will lead to this command structure:</p>
<div>
<pre class="pre-hl "><code class="ini">fastq_illumina_filter --keep [keep] -v -o [output_filtered] [input] > [stdout]</code></pre>
......@@ -429,7 +429,7 @@ class QIlluminaFilter (Analysis):
<h2>QIlluminaFilter template</h2>
<p>
To present the results of <code>QIlluminaFilter</code> analysis in the NG6 web interface, a template file must be written.
To present the results of <code>QIlluminaFilter</code> analysis in the NG6 web interface, a <a href="./core-analysis.html#analysis_template">template file</a> must be written.
To be associated to an analysis, a template file must have the exact same name as the <code>Python</code> class name of the
analysis, so the template file for <code>QIlluminaFilter</code> will be named <code>QIlluminaFilter.tpl</code>.
This template has to be written using <a target="_blank" href="http://www.smarty.net/">PHP Smarty</a> paradigm.
......@@ -807,7 +807,7 @@ class QFastQC (Analysis):
});</code></pre>
</div>
<p>
All analysis template files have access to a <code>bootstrap</code> modal with the id <code>ng6modal</code>.
All analysis template files have access to a <code>bootstrap</code> modal (dialog box/popup window) with the id <code>ng6modal</code>.
This modal is shown using <code>$("#ng6modal").modal();</code>. It also has 3 main parts that can be selected
and updated, each part with a uniq id:
</p>
......@@ -838,7 +838,7 @@ class QFastQC (Analysis):
<p>
Now that the analyses have been written, the <code>quickstart</code> NG6Workflow will be created to link those analyses together.
A NG6Workflow is a Python class defined in a <code>__init__.py</code> file in the workflows package. This class must inherit from
<code>ng6.ng6workflow.NG6Workflow</code> class, and must overload several methods:
<code>ng6.ng6workflow.NG6Workflow</code> class, and must overload several methods (more info <a href="./core-workflow.html#workflows">here</a>):
</p>
<ul>
<li><code>get_description()</code> to give a description to the workflow in the command line and in the interface.</li>
......@@ -906,7 +906,7 @@ class QuickStart(NG6Workflow):
<section id="fifth_step" class="group">
<h1 class="page-header">Step #5 <small>test your workflow</small></h1>
<p>
From your install directory enter
A nG6 workflow can be run from the command line (<code>ng6_cli.py</code>) or via the server (<code>ng6_server.py</code>). From your install directory enter
</p>
<div>
<pre class="pre-hl "><code class="ini">python bin/ng6_cli.py -h</code></pre>
......@@ -925,7 +925,7 @@ Available sub commands:
</p>
<div>
<pre class="pre-hl "><code class="ini">python2.7 bin/ng6_cli.py myquickstart --project-name "Demo project"
<pre class="pre-hl "><code class="ini">python bin/ng6_cli.py myquickstart --project-name "Demo project"
--name "my_quick_start" --description "quick start" --data-nature "DNA" --sequencer "Unknown"
--species "test" --type "quick start" --sample read1=/path/to/sample1_file.fastq.gz
--sample read1=/path/to/sample2_file.fastq.gz --admin-login &lt;login&gt;</code></pre>
......
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