#!/bin/bash #PBS -l select=1:ncpus=2 #PBS -l walltime=10:00:00 #PBS -q serial #PBS -P SHORTNAME #PBS -o /mnt/lustre/users/username/my_data/stdout.txt #PBS -e /mnt/lustre/users/username/my_data/stderr.txt #PBS -N TophatEcoli #PBS -M myemailaddress@someplace.com #PBS -m b module add chpc/BIOMODULES module add tophat/2.1.1 NP=`cat ${PBS_NODEFILE} | wc -l` EXE="tophat" ARGS="--num-threads ${NP} someindex reads1 reads2 -o output_dir" cd /mnt/lustre/users/username/my_data ${EXE} ${ARGS}