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<p> <img src="_static/logo.jpg" alt="logo"></p>

<h1>Welcome</h1>

<I>Ruffus</I> is a lightweight python module for writing computational pipelines.






<p>
It is designed to allow scientific analyses and other computational pipelines to 
be automated with the minimum of fuss and the least effort.
</p>    
<p>
This means that <I>ruffus</I> should be suitable for the simplest of tasks.
</p>
<p>
On the other hand, because it leaverages the full power of python, it should scale up to 
even fiendishly <A href= "complicated_example.html" complicated pipelines></A> 
which would cause makefile/ scons to go all cross-eyed and recursive, E.g. 
<ul class="simple">
<li>Multiply forking and rejoining dependencies </li>
<li>Indeterminate number of intermediate files</li>
<li>Sub-directories based on regular expression matches</li>
</ul>
    </p>

<p> Using <I>ruffus</I> requires only standard python syntax. Your 
    pipelined programmes can run in the same way without any "clever magic" 
    that you have to code around to customise. </p>

<p><I>Ruffus</I> tries very hard to be unintrusive. It has unambitiously 
lightweight syntax which tries to do one small thing well.
</p>

<p>I will be slowly adding in <a href="Todo.html"> more features 
    </a> while hopefully retaining the simple design. Please join me (email: 
    ruffus_lib at llew.org.uk) in setting the direction of this project if you 
    are interested.
</p>

<h1>Features</h1>
<p><I>Ruffus</I> provides automatic support for:</p>
<ul class="simple">
<li>Managing dependencies</li>
<li>Parallel jobs</li>
<li>Re-starting from arbitrary points, especially after errors</li>
<li>Display of the pipeline as a flowchart</li>
<li>Reporting</li>
</ul>

<h2> Documentation</h2>

<table class="contentstable" align="center" style="margin-left: 30px"><tr>
  <td width="50%">
    <p class="biglink"><a class="biglink" 
        href="Introduction.html">Introduction</a><br/>
    <span class="linkdescr">for an overview of <I>Ruffus</I></span></p>

    <p class="biglink"><a class="biglink" 
        href="contents.html">Contents</a><br/>
    <span class="linkdescr">for an overview of all the documentation</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>
  </td>
  
  <td width="50%">
       <p class="biglink"><a class="biglink" 
        href="simple_tutorial.html">Simple Tutorial</a><br/>
    <span class="linkdescr">for a quick introduction</span></p>
    <p class="biglink"><a class="biglink" 
        href="tutorial.html">Full tutorial</a><br/>
    <span class="linkdescr">for an-depth demonstration of all 
        <I>Ruffus</I> features</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>Get <I>Ruffus</I></h2>

<p>
    <i>Ruffus</i> is available as an <a 
    href="http://peak.telecommunity.com/DevCenter/EasyInstall">easy-install</a>able package on the <a href="http://pypi.python.org/pypi/ruffus">Python Package
    Index</a>.
  </p>
Just run:

<div class="highlight-python"><pre>easy_install ruffus</pre>
</div>
<p>or, to upgrade:</p>
<div class="highlight-python"><pre>easy_install -u ruffus</pre>
</div>
  
  
  <p>The <I>Ruffus</I> project is hosted at <a 
      href="http://code.google.com/p/ruffus">Google 
    Code</a></p>

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