#PBS -S /bin/csh
#PBS -N rpxx85-
#PBS -l cput=29:00:00,nodes=1:ppn=1
# run edscan in the batch mode on the PBS clusters (linux systems)
# submit the job using qsub *.job
# Primary PBS commands are in the path of /usr/pbs/bin
# To run the batch job you should include PBS commands in your default PATH
## set path= (/usr/pbs/bin $path)

if (! -d /usr/tmp/shuyun/rpxx85-) mkdir /usr/tmp/shuyun/rpxx85-
cd /usr/tmp/shuyun/rpxx85-
#/usr/bsd/hostname
#unlimit stack

# put all files in the correct path 
# In this example the path  is /usr/tmp/shuyun/rpxx85-   
/bin/rm -f trna* stab* bptab* seq *out
#
set PAT = '/home/lmb/shuyun/Pat'
cp $PAT/Ntrna85- .
cp $PAT/stab .
cp $PAT/bptab-4c .
cp /home/lmb/shuyun/seq/Bact/rpxx.seq  ./seq
echo "now running"

(time $PAT/patscan stab bptab-4c Ntrna85- seq Ntrna85-.scr  1.2 0.5 ) >& Ntrna85-.out

cp Ntrna85-.scr $PAT/rpxx
cp Ntrna85-.out  $PAT/rpxx

echo "patscan job was successfully completed"

/bin/rm -f *

cd ..
/bin/rmdir /usr/tmp/shuyun/rpxx85-

exit