|
1
|
1 ----------
|
|
|
2 | NAME |
|
|
|
3 ----------
|
|
|
4 S-MART
|
|
|
5
|
|
|
6
|
|
|
7 Description
|
|
|
8 -----------
|
|
|
9 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.
|
|
|
10
|
|
|
11 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.
|
|
|
12
|
|
|
13 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.
|
|
|
14
|
|
|
15
|
|
|
16 Instructions
|
|
|
17 ------------
|
|
|
18 Environment Installation :
|
|
|
19 1). Put the downloaded S-MART directories into your Galaxy tools directory.
|
|
|
20 2). Open .bashrc (if it dosen't exist, create one).
|
|
|
21 Write or add the S-MART directory path to PYTHONPATH :
|
|
|
22 export PYTHONPATH=S-MART_PATH:/usr/lib/python2.7/
|
|
|
23 (ex. export PYTHONPATH=/home/user/galaxy-dist/tools/smart_toolShed/)
|
|
|
24 3). Run .bashrc using . .bashrc command.
|
|
|
25
|
|
|
26 Supplementary Softwares :
|
|
|
27 Installation instructions and the user guide are available in the file "doc.pdf".
|
|
|
28
|
|
|
29
|
|
|
30 Copyright
|
|
|
31 ---------
|
|
|
32 Copyright INRA-URGI 2009-2013
|
|
|
33
|
|
|
34
|
|
|
35 Authors
|
|
|
36 -------
|
|
|
37 Matthias Zytnicki
|
|
|
38
|
|
|
39
|
|
|
40 Contact
|
|
|
41 -------
|
|
|
42 urgi-support@versailles.inra.fr
|
|
|
43
|
|
|
44
|
|
|
45 License
|
|
|
46 -------
|
|
|
47 This library is distributed under the terms of the CeCILL license
|
|
|
48 (http://www.cecill.info/index.en.html).
|
|
|
49 See the LICENSE.txt file.
|
|
|
50
|
|
|
51
|
|
|
52 Acknowledgements
|
|
|
53 ----------------
|
|
|
54 This product needs the following softwares :
|
|
|
55 * R, under the GNU General Public License
|
|
|
56 * MySQL, under the GNU General Public License
|
|
|
57 * Python, under the Python License, compatible with the GNU General Public License
|
|
|
58 * MySQL for Python, under the GNU General Public License
|
|
|
59 * Java, under the GNU General Public License
|
|
|
60
|
