The SNIT pipeline is available for download from www.bhsai.org/snit.html
Please perform the following steps to install the pipeline on a Linux/Unix machine:

1.	Download tarball from http://www.bhsai.org/snit.html 

2.	Extract the tarfile by typing	
		> tar -xvzf snit.tar.gz

3.	Download and install MUMmer
	a.	Download the latest version of MUMmer from http://sourceforge.net/projects/mummer/files/
	b.	Follow the installation instructions to install MUMmer

4.	Download and install Tandem Repeat Finder (TRF)
	a.	Download the appropriate Linux version of the TRF program from http://tandem.bu.edu/trf/trf.download.html
	b.	Follow the installation instructions for TRF

5.	Define environment variables and move TRF to the appropriate location
	a.	Point MUMMERDIR to the MUMmer installation. 
		eg: If MUMmer is installed under  /home/user/downloads/MUMmer3.22, 
		add the following line to your .bash_profile file (assuming you are in bash environment):
	 		export MUMMERDIR=/home/user/downloads/MUMmer3.22
	
	b.	Point SNIT_HOME to SNIT base directory. 
		eg: if you expanded SNIT under /home/user/downloads/Snit, 
		add the following to your .bash_profile file:
			export SNIT_HOME=/home/user/downloads/Snit
	
	c.	Add the SNIT build folder to your java CLASSPATH variable.
		eg: add the following to your .bash_profile file:
			export CLASSPATH=$SNIT_HOME/build:$CLASSPATH
	
	d.	Move/copy TRF to the $SNIT_HOME/bin folder: 
		Move the trf program to $SNIT_HOME/bin folder and rename it so that SNIT can find it. 
		eg: if the trf program you downloaded is named /home/user/downlaods/trf404.exe, execute the following command:
	 		mv /home/user/downlaods/trf404.exe $SNIT_HOME/bin/trf.exe

Note: The graphical interface for SNIT is implemented using java. Therefore, you will need 
to have the Java Runtime Environment (JRE 1.5+) installed.   The appropriate version of JRE can 
be downloaded from http://www.java.com/en/download/manual.jsp.

-- Refer to the README file for a complete set of instructions on installing and running SNIT
