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