LBMC » NucleoMiner

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Readme / Documentation for `NucleoMiner2`

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`NucleoMiner2` offers Python API and R package allowing to perform quantitative analysis of epigenetic marks on individual nucleosomes. It was developed to detect natural Single-Nucleosome Epi-Polymorphisms (SNEP) from MNase-seq and 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.

This software is provided with absolutely NO WARRANTY. The authors can not be held responsible, even partially, for any damage, loss, financial loss or any other undesired facts resulting from the use of the software.

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 are available here:

  - https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer

The Yvert lab web page is accessible here:

  - http://www.ens-lyon.fr/LBMC/gisv/

Installation

------------

The first installation step is to retrieve the source code of NucleoMiner2. You can do this by typing the following command in a terminal.

.. code:: bash

  git clone http://forge.cbp.ens-lyon.fr/git/nucleominer

..

Prerequisites

^^^^^^^^^^^^^

To work properly, NucleoMiner2 needs that the following free software are installed and made available on your system:

 - Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2

 - SAMtools http://samtools.sourceforge.net

 - bedtools http://code.google.com/p/bedtools/

 - TemplateFilter http://compbio.cs.huji.ac.il/NucPosition/TemplateFiltering

It also requires the following R packages to be installed on your system:

 - fork

 - rjson

 - seqinr

 - plotrix

 - DESeq

These packages can be installed by typing the following command in an R console:

.. code:: bash

   install.packages(c("fork", "rjson", "seqinr", "plotrix"))

   source("http://bioconductor.org/biocLite.R")

   biocLite("DESeq")

Finally,by typing the git command above, you downloaded specific R packages provided with NucleoMiner2 that you now need to install:

 - cachecache https://forge.cbp.ens-lyon.fr/redmine/projects/cachecache

 - bot https://forge.cbp.ens-lyon.fr/redmine/projects/bot

 - nucleominer https://forge.cbp.ens-lyon.fr/redmine/projects/nucleominer

To do so, type the following command in your terminal:     

.. code:: bash

  cd nucleominer

  R CMD INSTALL doc/Chuffart_NM2_workdir/deps/bot_0.14.tar.gz\

      doc/Chuffart_NM2_workdir/deps/cachecache_0.1.tar.gz\

      build/nucleominer_2.3.46.tar.gz