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38
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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 Copyright
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17 ---------
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18 Copyright INRA-URGI 2009-2013
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19
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20
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21 Authors
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22 -------
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23 Matthias Zytnicki
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24
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25
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26 Contact
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27 -------
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28 urgi-contact@versailles.inra.fr
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29
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30
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31 License
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32 -------
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33 This library is distributed under the terms of the CeCILL license
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34 (http://www.cecill.info/index.en.html).
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35 See the LICENSE.txt file.
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36
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37
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38 Installation under Galaxy
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39 -------------------------
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40 S-MART is available under the Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/
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41 Remember to set the variables "tool_config_file" and "tool_dependency_dir" accordingly. Please look up the Galaxy Tool Shed wiki to know more about it.
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42 It assumes you have R installed, as well as two packages: RColorBrewer (for colors in graphics), and Hmisc (for statistics). You can install them as root with the commands:
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43 - R --slave --no-save --no-restore --quiet -e 'if("RColorBrewer" %in% rownames(installed.packages()) == FALSE){install.packages("RColorBrewer", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
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44 - R --slave --no-save --no-restore --quiet -e 'if("Hmisc" %in% rownames(installed.packages()) == FALSE){install.packages("Hmisc", repos = c("http://cran.rstudio.com/"), dependencies = TRUE)}'
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45
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46 Optionally, you can organize the layout of S-MART tools following these instructions. This way, all the tools will be correctly sorted and appear in categories.
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47 - Locate the directory where S-MART has been installed: probably in "<galaxy install dir>/shed_tool/toolshed.g2.bx.psu.edu/repos/yufei-luo/s_mart/XXX/s_mart/"
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48 - Create a symbolic link "<galaxy install dir>/tools/s_mart" directing to "<S-MART install dir>/SMART/galaxy/"
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49 - Paste the content of "<S-MART install dir>/SMART/galaxy/tool_conf.xml" to your local "<galaxy install dir>/tool_conf.xml", for instance, right before the </toolbox> mark-up.
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50 - Remove the S-MART layout in "<galaxy install dir>/shed_tool_conf.xml" (the name may vary depending on your "universe_wgsi.ini" file) which has been automatically generated: remove the whole block between the markup <section id="s-mart" name="S-MART" version="XXX"> and the corresponding </section>.
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51 - Restart Galaxy to complete the install.
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52
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53
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54 Stand-alone installation
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55 ------------------------
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56 This product needs the following softwares :
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57 - R, under the GNU General Public License, and several R package (under the same License)
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58 - Python, under the Python License, compatible with the GNU General Public License
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59 - Java, under the GNU General Public License
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60
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61
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62 Instructions
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63 ------------
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64 Further installation instructions and the user guide are available in the file "doc.pdf".
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65
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66
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67 Acknowledgements
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68 ----------------
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69 Many thanks go helping developers:
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70 - Yufei Luo
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71 - the URGI team
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72 and the beta-testers:
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73 - Claire Toffano-Nioche
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74 - Claire Kuchly
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75 - among others...
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