#! /bin/bash #PBS -l select=1:ncpus=24 #PBS -l place=excl #PBS -l walltime=06:00:00 #PBS -q workq #PBS -o /home/username/lustre/some_reads/stdout.txt #PBS -e /home/username/lustre/some_reads/stderr.txt #PBS -M youremail@address.com #PBS -m be #PBS -N bowtiejob ################## MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH source /etc/profile.d/modules.sh #######module add module add bowtie2/2.2.2 NP=`cat ${PBS_NODEFILE} | wc -l` EXE="bowtie2" forward_reads="A_reads1.fq,B_reads_1.fq" reverse_reads="A_reads1.fq,B_reads_1.fq" output_file="piggy_hits.sam" ARGS="sscrofa --shmem --threads ${NP} --sam -q -1 ${forward_reads} -2 ${reverse_reads} ${output_file}" ${EXE} ${ARGS}