::::::::::::::
bowtie-align.pbs
::::::::::::::



#!/bin/sh

# SGI

#PBS -V
#PBS -N bowtie
#PBS -e bowtie.err
#PBS -o bowtie.out
#PBS -r n
#PBS -q high_mem
#PBS -l place=scatter
#PBS -l select=1:ncpus=1:host=n009
#PBS -l walltime=100:00:00

# shm, sock, ssm, rdma, rdssm
FABRIC=rdma
CORES=$[ `cat $PBS_NODEFILE | wc -l` ]
NODES=$[ `uniq $PBS_NODEFILE | wc -l` ]
cd $PBS_O_WORKDIR
printf "Current time is: `date`\n";
printf "Current PBS work directory is: $PBS_O_WORKDIR\n";
printf "Current PBS queue is: $PBS_O_QUEUE\n";
printf "Current PBS job ID is: $PBS_JOBID\n";
printf "Current PBS job name is: $PBS_JOBNAME\n";
printf "PBS stdout log is: $PBS_O_WORKDIR/sgi_mpitest.err\n";
printf "PBS stderr log is: $PBS_O_WORKDIR/sgi_mpitest.log\n";
printf "Fabric interconnect selected is: $FABRIC\n";
printf "This jobs will run on $CORES processors.\n";
. /etc/profile.d/modules.sh
module load mpt && echo "Successfully load modules"
TBEGIN=`echo "print time();" | perl`
printf "################################################\n";

/apps/bowtie -t -a --best -n 1 -l 5 -e 40 -y -p 32 --chunkmbs 16000 --nomaqround --al alignedReads.fq --un unalignedReads.fq --fullref -q --fr -S myIndex -1 long_1.fastq -2 long_2.fastq > /dev/null 2> bowtie-align.err
TEND=`echo "print time();" | perl`
printf "#################################################\n";
printf "+++ Job finished: `date`\n";
printf "+++ Job walltime: `expr $TEND - $TBEGIN`\n";
printf "#################################################\n";



::::::::::::::
bowtie-build.pbs
::::::::::::::



#!/bin/sh

# SGI

#PBS -V
#PBS -N bowtie
#PBS -e bowtie.err
#PBS -o bowtie.out
#PBS -r n
#PBS -q high_mem
#PBS -l place=scatter
#PBS -l select=1:ncpus=1:host=n009
#PBS -l walltime=100:00:00

# shm, sock, ssm, rdma, rdssm
FABRIC=rdma
CORES=$[ `cat $PBS_NODEFILE | wc -l` ]
NODES=$[ `uniq $PBS_NODEFILE | wc -l` ]
cd $PBS_O_WORKDIR
printf "Current time is: `date`\n";
printf "Current PBS work directory is: $PBS_O_WORKDIR\n";
printf "Current PBS queue is: $PBS_O_QUEUE\n";
printf "Current PBS job ID is: $PBS_JOBID\n";
printf "Current PBS job name is: $PBS_JOBNAME\n";
printf "PBS stdout log is: $PBS_O_WORKDIR/sgi_mpitest.err\n";
printf "PBS stderr log is: $PBS_O_WORKDIR/sgi_mpitest.log\n";
printf "Fabric interconnect selected is: $FABRIC\n";
printf "This jobs will run on $CORES processors.\n";
. /etc/profile.d/modules.sh
module load mpt && echo "Successfully load modules"
TBEGIN=`echo "print time();" | perl`
printf "################################################\n";

/apps/bowtie-build -f -o 6 -t 5 --little reference.fa myIndex > bowtie-build.txt
TEND=`echo "print time();" | perl`
printf "#################################################\n";
printf "+++ Job finished: `date`\n";
printf "+++ Job walltime: `expr $TEND - $TBEGIN`\n";
printf "#################################################\n";



::::::::::::::
bowtie-check.pbs
::::::::::::::



#!/bin/sh

# SGI

#PBS -V
#PBS -N bowtie
#PBS -e bowtie.err
#PBS -o bowtie.out
#PBS -r n
#PBS -q high_mem
#PBS -l place=scatter
#PBS -l select=1:ncpus=1:host=n009
#PBS -l walltime=100:00:00

# shm, sock, ssm, rdma, rdssm
FABRIC=rdma
CORES=$[ `cat $PBS_NODEFILE | wc -l` ]
NODES=$[ `uniq $PBS_NODEFILE | wc -l` ]
cd $PBS_O_WORKDIR
printf "Current time is: `date`\n";
printf "Current PBS work directory is: $PBS_O_WORKDIR\n";
printf "Current PBS queue is: $PBS_O_QUEUE\n";
printf "Current PBS job ID is: $PBS_JOBID\n";
printf "Current PBS job name is: $PBS_JOBNAME\n";
printf "PBS stdout log is: $PBS_O_WORKDIR/sgi_mpitest.err\n";
printf "PBS stderr log is: $PBS_O_WORKDIR/sgi_mpitest.log\n";
printf "Fabric interconnect selected is: $FABRIC\n";
printf "This jobs will run on $CORES processors.\n";
. /etc/profile.d/modules.sh
module load mpt && echo "Successfully load modules"
TBEGIN=`echo "print time();" | perl`
printf "################################################\n";

/apps/bowtie-inspect -v -s myIndex > bowtie-inspect.txt

TEND=`echo "print time();" | perl`
printf "#################################################\n";
printf "+++ Job finished: `date`\n";
printf "+++ Job walltime: `expr $TEND - $TBEGIN`\n";
printf "#################################################\n";