FastHMM/FastBLAST Installation Guide

Before you try to install FastHMM and FastBLAST, you should already
have installed NCBI BLAST, HMMer, MUSCLE, and CD-HIT. If you are not
using a UNIX machine, you will also need to install UNIX-like tools
(e.g. cygwin). You will also need to be able to run make (preferably
GNU make) and a C compiler (e.g., gcc).

The next step is to expand the fasthmm tarball to create the main
fasthmm directories (you may have already done this), e.g.:

	cd ~
	tar xzf fasthmm-1.3.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-1.3
	./install.pl  -prefix . -out ~/fasthmm

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. install.pl places symbolic links to the
executables into fasthmm/bin, so if you move the tools, you'll need to
rerun install.pl. (Also, this part of install.pl might not work
correctly on non-UNIX machines.)

The next step is to build the executables:
	cd ~/fasthmm
	make

You may need to redefine the CC variable in the Makefile to match the
C compiler that you have installed.

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 and to expand them. Note
that you should do this inside your fasthmm/db directory. E.g. to
download and install pfam,

	cd ~/fasthmm/db
	wget pfam.tar.gz
	tar xzf pfam.tar.gz

There is one tarball for each database of HMMs
(gene3d,panther,pfam,pirsf,smart,superfam,tigrfam). There is also a
tarball of COG to use with the COGHits.pl script.  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. If you install them somewhere
else, you can use the -d option to fastHmm.pl to use them.

For information on how to run FastHMM and FastBLAST, please see the documentation
at http://microbesonline.org/fasthmm

To test that FastBLAST is installed correctly, set FASTHMM_DIR and run the fbtest, e.g.

	export FASTHMM_DIR=~/fasthmm
	cd $FASTHMM_DIR
	make -f fbtest

This should succeed and the log should end the statements:

	Wrote ./fb.all.nseq
	Wrote DB table ./fb.all.align.seek.db with indexes to alignments for 5 domains
	Wrote DB table ./fb.all.domains.bygene.seek.db with indexes to domains for 6 genes
	make[1]: Leaving directory `~/fasthmm/fbtest'

FastHMM takes a significant time to run, even on small data sets,
because it issues many jobs. Also, the correct output changes as the
databases change. So, there is no test script for FastHMM.

If you need assistance, please email us at
fasthmm@microbesonline.org.