module load bioinformatics/prottest
module load bioinformatics/phylip/3.69
module load bioinformatics/raxml/7.3.0-SSE3-gcc
module load perl/5.15.8
module load bioinformatics/bio-hal/biohal

cd /sw/bioinformatics/bio-hal/src/bio-hal
tar -zxvf bio-hal.tar.gz
cd /sw/bioinformatics/bio-hal/trunk
/sw/bioinformatics/bio-hal/trunk/requirements.pl

Install all the required software!