Before running your scripts remember to run¹⁾:

user@login01:~ $ module add bowtie/1.0.0

Then your job script called my_job.msub will look something like this:

my_job.msub

#/bin/sh
#MSUB -l procs=64
#MSUB -l feature=dell
#MSUB -l walltime=10:00:00
#MSUB -m be
#MSUB -V
#MSUB -o ${HOME}/scratch5/BOWTIE/stdout.txt
#MSUB -e ${HOME}/scratch5/BOWTIE/stderr.txt
#MSUB -d ${HOME}/scratch5/BOWTIE/
#MSUB -N MyGromacsJob
#MSUB -mb
 
NP=`cat ${PBS_NODEFILE} | wc -l`
 
EXE=bowtie
ARGS="-s input.tpr -deffnm input.tpr"
 
mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}

Finally submit your job using:

user@login01:~ $ msub my_job.msub