diff SMART/Java/README.txt @ 18:94ab73e8a190

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+----------
+|  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
+-------
[e-mail]
+
+
+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...