view smart_toolShed/README.txt @ 1:30c5431d8ce4

author yufei-luo
date Thu, 17 Jan 2013 11:01:51 -0500
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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 :
Installation instructions and the user guide are available in the file "doc.pdf".

Copyright INRA-URGI 2009-2013

Matthias Zytnicki


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

This product needs the following softwares :
 * R, under the GNU General Public License
 * MySQL, under the GNU General Public License
 * Python, under the Python License, compatible with the GNU General Public License
 * MySQL for Python, under the GNU General Public License
 * Java, under the GNU General Public License