|
6
|
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/s_mart/)
|
|
|
24 3). Run .bashrc using . .bashrc command.
|
|
|
25
|
|
|
26 Supplementary Softwares :
|
|
|
27 * R, under the GNU General Public License
|
|
|
28 * Python, under the Python License, compatible with the GNU General Public License
|
|
|
29 Installation instructions and the user guide are available in the file
|
|
|
30 "documentation.pdf".
|
|
|
31
|
|
|
32
|
|
|
33 Copyright
|
|
|
34 ---------
|
|
|
35 Copyright INRA-URGI 2009-2013
|
|
|
36
|
|
|
37
|
|
|
38 Authors
|
|
|
39 -------
|
|
|
40 Matthias Zytnicki
|
|
|
41 Yufei Luo
|
|
|
42
|
|
|
43 Contact
|
|
|
44 -------
|
|
|
45 urgi-support@versailles.inra.fr
|
|
|
46
|
|
|
47
|
|
|
48 License
|
|
|
49 -------
|
|
|
50 This library is distributed under the terms of the CeCILL license
|
|
|
51 (http://www.cecill.info/index.en.html).
|
|
|
52 See the LICENSE.txt file.
|
|
|
53
|
|
|
54
|
|
|
55 Acknowledgements
|
|
|
56 ----------------
|
|
|
57 Yufei Luo was supported by the Plant Breeding and Genetics research division of
|
|
|
58 the INRA, and by the Groupement d'intérêt scientifique IBISA.
|
