FastHmm Installation Guide

Before you try to install FastHmm, you should already have installed
NCBI BLAST, HMMer, MUSCLE, and CD-HIT. The next step is to expand the
fasthmm tarball to create the main fasthmm directories (you may have
already done this):

	cd ~
	tar xzf fasthmm-1.0.tar.gz

Then you need to run the install script, which populates the fasthmm
directories with files and also creates symbolic links in the
fasthmm/bin directory to the actual tool executables:

	cd ~/fasthmm-1.0
	./install.pl  -prefix ~/fasthmm-1.0

By default, install.pl looks for the relevant tools in your path, but
you can tell it to look elsewhere. Run install.pl without arguments
for more information.

Finally, you need to populate fasthmm/db directory with databases of
protein families. The easiest way to do this is to download the tar
files from http://microbesonline.org/fasthmm, e.g. to download and
install pfam,

	cd ~/fasthmm-1.0/fasthmm/db
	wget http://microbesonline.org/fasthmm/release/fasthmm_pfam_20070723_db.tar.gz
	tar xzf fasthmm_pfam_20070723_db.tar.gz

Unfortunately, these tar files are rather large: the tar files total
nearly 3 gigabytes, and they take up another 12 gigabytes when
installed. If you wish to run fasthmm on your own set of families, see
the fasthmm/db/README file for instructions.

For additional assistance, please contact the fastHmm/fastBlast team
at http://microbesonline.org/fasthmm or by email to
fasthmm@microbesonline.org.