#!/bin/bash
#You will need to edit these paths to match your installation - see README_DomFOLD
export PSIBLAST=/home/Liam/programs/blast-2.2.13/bin/blastpgp
export BLAST_DB=/home/Liam/data/blastdb/nrfilt
export HHSEARCH_HOME=/home/Liam/programs/bin/
export HHSEARCH_CAL=/home/Liam/data/hhsearch/cal.hhm
export HHSEARCH_DB=/home/Liam/data/hhsearch/hhsearch_db.hhm
export KEY_MODELLER9v4=XXXXXXXXXXXX
export MODELLER=/usr/bin/mod9v5
export PDP=/home/Liam/programs/bin/pdp
export DISOPRED=/home/Liam/programs/disopred2/bin/disopred
export DISOPRED_DB=/home/Liam/programs/disopred2/data/
export JAVA_HOME=/home/Liam/jdk1.5.0_06/

if [ -e $PSIBLAST ] && [ -e $BLAST_DB ] && [ -e $HHSEARCH_HOME ] && [ -e $HHSEARCH_CAL ] && [ -e $HHSEARCH_DB ] && 
[ -e $MODELLER ] && [ -e $PDP ] && [ -e $DISOPRED ] && [ -e $DISOPRED_DB ] && [ -e $JAVA_HOME ]
then
	$JAVA_HOME/bin/java -jar DomFOLD.jar $1 $2 $3
else
	echo "Please double check that all of your paths are set correctly."
	exit 1
fi