{% extends "layout.html" %}
{% set title = 'SphinxReport' %}

{% block body %}

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

<h1>Welcome</h1>

<i>SphinxReport</i> is a report generator that is implemented as an extension
to <a href="http://sphinx.pocoo.org/">Sphinx</a>.

<p>
Its purpose is to facilitate writing scientific reports interpreting large and changing datasets. It is
designed to assist the iterative analysis during the development of a
computational scientific pipeline as understanding of the data grows.
Once the pipeline settles down, <i>SphinxReport</i> permits an easy transition
towards the automatic report generation needed when the pipeline is
run on new data sets.
<p>
<i>SphinxReport</i> is easy to use and powerful
enough to give all the flexibility needed during the development of computational pipelines and robustness during the
production use of a pipeline.
It is intended for developers and computational scientists with <a href="http://www.python.org">python</a>
scripting experience.
<p>
<i>SphinxReport</i> comes with all the batteries included thanks to <a href="http://www.python.org">python</a> and <a href="http://sphinx.pocoo.org/">Sphinx</a>,
in particular, it
<ul>
<li>uses simple markup in the form of <a href="http://docutils.sourceforge.net/rst.html">restructured text</a>,
<li>supports both automated and narrative analysis,
<li>keeps code, data and text together,
<li>takes care of indexing and formatting to produce something presentable,
<li>produces static html, latex, ps and pdf.
</ul>

<h2>How to get Sphinx</h2>

To install sphinx, simply type:

<p>
pip install SphinxReport
</p>

Sphinx source code is available on <A href="https://github.com/AndreasHeger/sphinx-report">github</A>.
The latest release can be found on <A href="https://pypi.python.org/pypi/SphinxReport">pypi</A>.

<h2> Documentation</h2>

<table class="contentstable" align="center" style="margin-left: 30px"><tr>
  <td width="50%">
    <p class="biglink"><a class="biglink" href="contents.html">Contents</a><br/>
    <span class="linkdescr">for a complete overview</span></p>
    <p class="biglink"><a class="biglink" href="search.html">Search page</a><br/>
    <span class="linkdescr">search the documentation</span></p>
  </td><td width="50%">
    
    <p class="biglink"><a class="biglink" href="genindex.html">General Index</a><br/>
    <span class="linkdescr">all functions, classes, terms</span></p>
    <p class="biglink"><a class="biglink" href="modindex.html">Module Index</a><br/>
    <span class="linkdescr">quick access to all documented modules</span></p>
  </td></tr>
</table>

<h2>Examples</h2>

<B><A HREF="../SphinxReportExamples/rnaseq/contents.html">RNA-Seq report</A></B> - 
a report generated from the <A HREF='http://www.cgat.org'>CGAT</A>
<A HREF="http://en.wikipedia.org/wiki/RNA-Seq">RNA-Seq</A> analysis pipeline using the data from
<A HREF="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24399">Yang et. al. 2011</A>.

<h2>Get SphinxReport</h2>

<p>
    <i>SphinxReport</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/Sphinx">Python Package
    Index</a>.
  </p>
  <p>The code can be found at <a href="http://code.google.com/p/sphinx-report">Google Code</a>, at
    <tt>http://code.google.com/p/sphinx-report/</tt>.
</p>

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