view smart_toolShed/README.txt @ 4:1fc014126d55

author yufei-luo
date Fri, 18 Jan 2013 04:45:50 -0500
parents 4eaf0e192d11
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|  NAME  |

Several tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have developed a toolbox, S-MART, which handles mapped RNA-Seq and ChIP-Seq data.

S-MART is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

S-MART does not require a computer science background and thus can be used by all biologists through a graphical interface. S-MART can run on any personal computer, yielding results within an hour for most queries. 

Environment Installation :
1). Put the downloaded S-MART directories into your Galaxy tools directory.
2). Open .bashrc (if it dosen't exist, create one).
Write or add the S-MART directory path to PYTHONPATH :
export PYTHONPATH=S-MART_PATH:/usr/lib/python2.7/
(ex. export PYTHONPATH=/home/user/galaxy-dist/tools/smart_toolShed/)
3). Run .bashrc using . .bashrc command.

Supplementary Softwares :
 * R, under the GNU General Public License
 * Python, under the Python License, compatible with the GNU General Public License
Installation instructions and the user guide are available in the file

Copyright INRA-URGI 2009-2013

Matthias Zytnicki
Yufei Luo


This library is distributed under the terms of the CeCILL license 
See the LICENSE.txt file.

Yufei Luo was supported by the Plant Breeding and Genetics research division of
the INRA, and by the Groupement d'intérêt scientifique IBISA.