#! /bin/sh
#SLURM -N 1
#SLURM -o msa.out
#
set -x
ulimit -c unlimited

ORIGDIR=`pwd`
PID=$$
export PID
TMPDIR=/scratch/$USER/$PID
export TMPDIR
mkdir -p $TMPDIR
cd $TMPDIR
#
# Copy: $ORIGDIR/seq.pir
# to: seq.pir
#
cp $ORIGDIR/seq.pir seq.pir
#
srun /biomed/bin/msa_10_1000 -H heur.msf -O opt.msf -b seq.pir > \
          carp_r_5_msa_10_1000_msa250.out 
#
# Copy: carp_r_5_msa_10_1000_msa250.out
# to: $ORIGDIR/carp_r_5_msa_10_1000_msa250.out
#
cp carp_r_5_msa_10_1000_msa250.out \
          $ORIGDIR/carp_r_5_msa_10_1000_msa250.out
#
# Check copy of carp_r_5_msa_10_1000_msa250.out
# If not, then write the present directory into
# the cpr file to help find the output files.
#
if [ $? -eq 0 ]
   then
        echo " "
        echo "Successfully copied carp_r_5_msa_10_1000_msa250.out"
        echo " "
   else
        test -f carp_r_5_msa_10_1000_msa250.out
        if [ $? -eq 0 ]
           then
               echo "PROBLEM IN COPY OF carp_r_5_msa_10_1000_msa250.out"
               pwd
               far mkdir $PID  
               far store carp_r_5_msa_10_1000_msa250.out \
                    $PID/carp_r_5_msa_10_1000_msa250.out
           else
               echo "The file carp_r_5_msa_10_1000_msa250.out does not exist."
           fi
        echo " "
   fi
#
#
# Copy: heur.msf
# to: $ORIGDIR/carp_r_5_msa_10_1000_msa250_heuristic.msf
#
cp heur.msf \
          $ORIGDIR/carp_r_5_msa_10_1000_msa250_heuristic.msf
#
# Check copy of heur.msf
# If not, then write the present directory into
# the cpr file to help find the output files.
#
if [ $? -eq 0 ]
   then
        echo " "
        echo "Successfully copied heur.msf"
        echo " "
   else
        test -f heur.msf
        if [ $? -eq 0 ]
           then
               echo "PROBLEM IN COPY OF heur.msf"
               pwd
               far mkdir $PID  
               far store heur.msf $PID/heur.msf
           else
               echo "The file heur.msf does not exist."
           fi
        echo " "
   fi
#
#
# Copy: opt.msf
# to: $ORIGDIR/carp_r_5_msa_10_1000_msa250_optimal.msf
#
cp opt.msf \
          $ORIGDIR/carp_r_5_msa_10_1000_msa250_optimal.msf
#
# Check copy of opt.msf
# If not, then write the present directory into
# the cpr file to help find the output files.
#
if [ $? -eq 0 ]
   then
        echo " "
        echo "Successfully copied opt.msf"
        echo " "
   else
        test -f opt.msf
        if [ $? -eq 0 ]
           then
               echo "PROBLEM IN COPY OF opt.msf"
               pwd
               far mkdir $PID  
               far store opt.msf $PID/opt.msf
           else
               echo "The file opt.msf does not exist."
           fi
        echo " "
   fi
#
cd $ORIGDIR 
/bin/rm -rf $TMPDIR