--- a/SMART/Java/README.txt	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/Java/README.txt	Tue Apr 30 14:33:21 2013 -0400
@@ -13,9 +13,14 @@
 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. 
 
 
+Instructions
+------------
+Installation instructions and the user guide are available in the file "doc.pdf".
+
+
 Copyright
 ---------
-Copyright INRA-URGI 2009-2013
+Copyright INRA-URGI 2009-2010
 
 
 Authors
@@ -35,41 +40,12 @@
 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...
+This product needs the following softwares :
+ * R, under the GNU General Public License
+ * MySQL, under the GNU General Public License
+ * Python, under the Python License, compatible with the GNU General Public License
+ * MySQL for Python, under the GNU General Public License
+ * Java, under the GNU General Public License
+