----------
|  NAME  |
----------
S-MART


Description
-----------
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.

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.

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. 


Copyright
---------
Copyright INRA-URGI 2009-2013


Authors
-------
Matthias Zytnicki


Contact
-------
urgi-contact@versailles.inra.fr


License
-------
This library is distributed under the terms of the CeCILL license 
(http://www.cecill.info/index.en.html).
See the LICENSE.txt file.


Installation under Galaxy
-------------------------
S-MART is available under the Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/
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.
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:
 - 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)}'
 - 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)}'

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.
 - 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/"
 - Create a symbolic link "<galaxy install dir>/tools/s_mart" directing to "<S-MART install dir>/SMART/galaxy/"
 - 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.
 - 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>.
 - Restart Galaxy to complete the install.


Stand-alone installation
------------------------
This product needs the following softwares :
 - R, under the GNU General Public License, and several R package (under the same License)
 - Python, under the Python License, compatible with the GNU General Public License
 - Java, under the GNU General Public License


Instructions
------------
Further installation instructions and the user guide are available in the file "doc.pdf".


Acknowledgements
----------------
Many thanks go helping developers:
 - Yufei Luo
 - the URGI team
and the beta-testers:
 - Claire Toffano-Nioche
 - Claire Kuchly
 - among others...
