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{% extends "layout.html" %}
{% set title = 'Ruffus' %}
{% block extrahead %}
<meta content='Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics' name='description'/>
<meta content='python, pipeline, computation, cluster, Ruffus, bioinformatics, parallel' name='keywords'/>
<meta content='Leo Goodstadt' name='Author'/>
<meta content='Leo Goodstadt' name='Publisher'/>
<meta content='ruffus@llew.org.uk' name='Email'/>
<meta content='index, follow' name='robots'/>
<meta content='en-uk' name='language'/>
<meta content='United Kingdom' name='country'/>
<meta name='copyright' content='cgat-developers'/>
{% endblock %}
{% block body %}
<p>
<a href="why_ruffus.html#why-ruffus"> <img src="_images/logo.jpg" alt="logo"></a>
</p>
Ruffus is a Computation Pipeline library for python. It is open-sourced,
powerful and user-friendly, and widely used in science and bioinformatics.<br/><br/>
<h1>Citation:</h1>
<blockquote>
Please cite <I>Ruffus</I> as:<br/>
<div><a class="reference external" href="http://bioinformatics.oxfordjournals.org/content/early/2010/09/16/bioinformatics.btq524">Leo Goodstadt (2010)</a> :
<strong>Ruffus: a lightweight Python library for computational pipelines.</strong> <em>Bioinformatics</em> 26(21): 2778-2779</div></blockquote><br/>
<h1>Welcome</h1>
<table class="Introduction" align="center" style="margin-left: 30px">
<tr>
<td width="50%">
<p><I>Ruffus</I> is designed to allow scientific and other analyses to
be automated with the minimum of fuss and the least effort.</p>
These are <I>Ruffus</I>'s strengths:
<ul>
<li><b>Lightweight</b>: Suitable for the simplest of tasks</li>
<li><b>Scalable</b>: Handles even fiendishly complicated pipelines</a>
which would cause <i>make</i> or <i>scons</i> to go cross-eyed and recursive.</li>
<li><b>Standard python</b>: No "clever magic", no pre-processing. </li>
<li><b>Unintrusive</b>: Unambitious, lightweight syntax which tries to do this
one small thing well. </li>
</ul>
<p>Please join me (email: ruffus_lib at llew.org.uk) in setting the direction of
this project if you are interested.
</p>
</td>
<td width="50%">
<img src="_images/front_page_flowchart.png" alt="flowchart">
</td>
</tr>
</table>
<h1> Documentation</h1>
<table class="contentstable" align="center" style="margin-left: 30px">
<tr>
<td width="50%">
<p class="biglink"><a class="biglink"
href="installation.html">Download</a><br/>
<span class="linkdescr">to install <I>Ruffus</I></span></p>
<p class="biglink"><a class="biglink"
href="tutorials/new_tutorial/introduction.html">Simple Tutorial</a><br/>
<span class="linkdescr">Start here for a quick introduction to <i>Ruffus</i></span></p>
<p class="biglink"><a class="biglink"
href="tutorials/new_tutorial/manual_contents.html">Manual</a>
<a class="biglink" href="_downloads/ruffus.pdf">(pdf)</a><br/>
<span class="linkdescr">for an-depth demonstration of all
<I>Ruffus</I> features</span></p>
</td>
<td width="50%">
<p class="biglink"><a class="biglink"
href="contents.html">Table of contents</a><br/>
<span class="linkdescr">for an complete listing of all the documentation</span></p>
<p class="biglink"><a class="biglink"
href="faq.html">Frequently Answered Questions</a><br/>
<span class="linkdescr">for any common problems, clever solutions from the community</span></p>
<p class="biglink"><a class="biglink"
href="design.html">Design</a><br/>
<span class="linkdescr">to understand the design of <I>Ruffus</I></span></p>
<p class="biglink"><a class="biglink"
href="cheatsheet.html">Cheat Sheet</a><br/>
<span class="linkdescr">for Ruffus syntax</span></p>
</td>
</tr>
</table>
<h2>Install <I>Ruffus</I></h2>
<p>
<i>Ruffus</i> is available as a <a
href="">conda package</a>able package on the <a href="http://pypi.python.org/pypi/ruffus">Python Package
Index</a>.
</p>
Just run:
<div style="margin-left: 30px" class="highlight-python"><pre>conda install -c bioconda ruffus</pre>
</div>
or
<div style="margin-left: 30px" class="highlight-python"><pre>pip install ruffus</pre>
</div>
<br>
<p>
The very latest (in development) code can be obtained via <a href="https://github.com/cgat-developers/ruffus"> git </a>:
<div style="margin-left: 30px" class="highlight-python"><pre>git clone https://github.com/cgat-developers/ruffus.git</pre>
</div>
</p>
<h1>Feedback and Getting Involved:</h1>
<p>We would love your input and involvment. If you find a bug or would like to request an improvement
please raise a github issue. for more information on how to contribute code please see the
<a href="contributing.html"> contributing </a> section for more information on how to
contribute to the project</p>
{% endblock %}
|
