qsub script for running velvet on SGE cluster

velvet.qsub.sh

#!/bin/sh

#$ -N velvet
#$ -m e
#$ -e sge_velvet.err
#$ -o sge_velvet.out
#$ -M adavisr@ufl.edu
#$ -q all.q
#$ -l mem_free=4G

JOB_ID=$1
PREFIX=velvet_out/$1

mkdir -p velvet_out/
mkdir -p $PREFIX

for kmer in 17 31
do
    echo "# INPUT  = $1"
    echo "# OUTPUT = $PREFIX"
    echo "# L_KMER = $kmer"

    mkdir -p $PREFIX/velvet_$kmer/
    velveth $PREFIX/velvet_$kmer/ $kmer -fasta -short $1 > $PREFIX/velvet_$kmer/velveth.log
    velvetg $PREFIX/velvet_$kmer > $PREFIX/velvet_$kmer/velvetg.log

    echo "#################################################################"
done