Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/README.txt @ 1:30c5431d8ce4
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| author | yufei-luo |
|---|---|
| date | Thu, 17 Jan 2013 11:01:51 -0500 |
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| 0:e0f8dcca02ed | 1:30c5431d8ce4 |
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| 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 |