This document contains the installation and example run instructions
for GISTIC compiled for 64-bit linux.  

#####################################################
To install GISTIC

1) Copy the file "GISTIC_2_0_0.tar.gz" to the directory where you want to
   install GISTIC.

	 cp GISTIC_2_0_0.tar.gz <gistic_install_dir>
	   
2) Unpack the installation file:

	 tar zxf GISTIC_2_0_0.tar.gz -p

3) In order to run this executable, MATLAB Component Runtime version 7.14 
   Component Runtime (MCR) must be installed on your computer.  If the
   MCR is already installed, locate it on your system.  We will call
   the location of the MCR installation <mcr_root> in the rest of this
   documentation.  

   If the MCR is not installed, you must install it by running
   MCRInstaller.bin, which is located in the gistic_install_dir.

          cd <gistic_install_dir>
	  ./MCRInstaller.bin
	  
   The installation asks you to name the directory where you would
   like the matlab runtime components to install.  The quickstart
   example at the end of this documentation assumes that the MCR is
   installed in: <gistic_install_dir>/MATLAB_Component_Runtime

   If you choose a different directory for the MCR components and
   still wish to run the "run_gistic_example" script, you must modify
   the section of the "run_gistic_example" script that sets the LD_LIBRARY_PATH
   and XAPPLRESDIR environment variables.


4) In order to run gistic, you must set the environment variables.
   The following can be added to your login script if you do not wish to set
   your environment variables each time you open a new shell.

###### FILL IN <mcr_root> HERE #####
set mcr_root = <mcr_root> $thisdir/MATLAB_Component_Runtime
setenv LD_LIBRARY_PATH $mcr_root/v714/runtime/glnxa64:$LD_LIBRARY_PATH
setenv LD_LIBRARY_PATH $mcr_root/v714/sys/os/glnxa64:$LD_LIBRARY_PATH
setenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:$LD_LIBRARY_PATH
setenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:$LD_LIBRARY_PATH
setenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATH
setenv XAPPLRESDIR $mcr_root/v714/X11/app-defaults
#####################################

A GISTIC Run from Example Files

This zip file includes example files for a complete GISTIC run.  After
you have installed GISTIC using the instructions above, you can run
the example from the <gistic_install_directory>:

    ./run_gistic_example

Note that if your MCR has been installed in a location other than
<gistic_install_directory>/MATLAB_Component_Runtime you will need to
modify the mcr_root variable in the example script to point to the 
correct location.