Repeat masker

5.  Install RepeatMasker. Download from http://www.repeatmasker.org
	a.  The most current version of RepeatMasker requires a program called TRF.
	This can be downloaded from http://tandem.bu.edu/trf/trf.html
	b.  The TRF download will contain a single executable file.  You will need to
	rename the file from whatever it is to just 'trf' (all lower case).
	c.  Make TRF executable by typing chmod +x+u trf.  You can then move this file
	wherever you want.  I just put it in the /RepeatMasker directory.
	d.  Unpack RepeatMasker to the directory of your choice (i.e. /usr/local).
	e.  If you do not have WuBlast installed, you will need to install the program
	RMBlast.  We do not recomend using cross_match, as RepeatMasker
	performance will suffer.
	f.  Now in the RepeatMasker directory type perl ./configure in the command
	line. You will be asked to identify the location of perl, wublast, and
	trf.  The script expects the paths to the folders containing the
	executables (because you are pointing to a folder the path must end in a
	'/' character or the configuration script throws a fit).
	g.  Add the location where you installed RepeatMasker to your PATH variable in
	.bash_profile (i.e. export PATH="/usr/local/RepeatMasker:$PATH").
	h.  You must register at http://www.girinst.org and download the Repbase
	repeat database, Repeat Masker edition, for RepeatMasker to work.
	i.  Unpack the contents of the RepBase tarball into the RepeatMasker/Libraries
	directory.