Readme / Documentation for *NucleoMiner2*
*****************************************

*NucleoMiner2* offers Python API and R package allowing to perform
quantitative analysis of nucleosomal epigenome. It is especially well
suited for scripting to extract natural Single-Nucleosome Epi-
Polymorphisms (SNEP) from ChIP-Seq data.


License
=======

Copyright CNRS 2012-2013

* Florent CHUFFART

* Jean-Baptiste VEYRIERAS

* Gael YVERT

This software is a computer program which purpose is to perform
quanti- tative analysis of epigenetic marks at single nucleosome
resolution.

This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software.  You can  use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided
only with a limited warranty  and the software's author,  the holder
of the economic rights,  and the successive licensors  have only
limited liability.

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards
their requirements in conditions enabling the security of their
systems and/or data to be ensured and,  more generally, to use and
operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.


Installation Instructions
=========================


Links
-----

*NucleoMiner2* home page and documentation: https://forge.cbp.ens-
lyon.fr/redmine/projects/nucleominer

Gael Yvert lab page: http://www.ens-lyon.fr/LBMC/gisv/


Installation
------------

   * Download archive

   * Compile bowtie2

   * Compile samtools

   * Compile bedtools

   * Compile TemplateFilter

Required R pacakes:
   * bot - fork

   * rjson

   * seqinr

   cd src/r_packages/
         tar xfvz R-latest.tar.gz
         cd R-patched
         ./configure --with-x=no PDFLATEX="ls"
         make
   cd ../../..
   R_BIN=src/r_packages/R-patched/bin/R
         $R_BIN CMD INSTALL src/r_packages/rjson_0.2.12.tar.gz
         $R_BIN CMD INSTALL src/r_packages/seqinr_3.0-7.tar.gz
         $R_BIN CMD INSTALL src/r_packages/plotrix_3.4-5.tar.gz
         $R_BIN CMD INSTALL src/r_packages/nm_2.0.tar.gz
         $R_BIN CMD INSTALL src/r_packages/fork_1.2.4.tar.gz
         $R_BIN CMD INSTALL src/r_packages/bot_0.9.tar.gz
         $R_BIN CMD INSTALL src/r_packages/DESeq_1.14.0.tar.gz

...


usage
=====

See html documentation for *NucleoMiner2*: http://www.ens-
lyon.fr/LBMC/gisv/