========================
Galaxy wrapper for MACS2
========================

With the improvement of sequencing techniques, chromatin immunoprecipitation 
followed by high throughput sequencing (ChIP-Seq) is getting popular to study 
genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq 
analysis method, we present a novel algorithm, named Model-based Analysis of 
ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures 
the influence of genome complexity to evaluate the significance of enriched ChIP 
regions, and MACS improves the spatial resolution of binding sites through 
combining the information of both sequencing tag position and orientation. 
MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.


============
Installation
============

It is recommended to install this wrapper via the `Galaxy Tool Shed`.

.. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2


=======
History
=======
- v2.0.10.1: Initial public release
- v2.0.10.3: add "broad peaks" options


====================
Detailed description
====================

View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst


===============================
Wrapper Licence (MIT/BSD style)
===============================

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.