#! /bin/sh
#SLURM -N 1
#SLURM -o nwgap.out

set -x
ulimit -c unlimited

ORIGDIR=`pwd`
PID=$$
export PID
TMPDIR=/scratch/$USER/$PID
export TMPDIR
mkdir -p $TMPDIR
cd $TMPDIR
#
# Copy: $ORIGDIR/hahu.seq
# to: hahu.seq
#
cp $ORIGDIR/hahu.seq hahu.seq
#
# Copy: $ORIGDIR/halua.seq
# to: halua.seq
#
cp $ORIGDIR/halua.seq halua.seq
#
#
# Run program      nwgap with the input coming
# From the following *HERE* Document.
# (NOTE: This is shell specific!)
#
srun    /biomed/bin/nwgap <<\EOF
ECHO
TITLE Comparisons of two hemoglogin alpha chain sequences, HAHU & HALUA
SEQUENCE QUERY=hahu.seq
SEQUENCE LIBRARY=halua.seq
SEQUENCE RESULT=hahu_nwgap_halua_pam250.out
WIDTH=80
ALPHABET PROTEIN
SCORE PAM250, GAP=-1, NEWGAP=-8
SHOW
MATCH ALL
QUIT
EOF
#
# This is the end of the input file.

#        echo " "
ls -la
#
#
# Copy: hahu_nwgap_halua_pam250.out
# to: $ORIGDIR/hahu_nwgap_halua_pam250.out
#
cp hahu_nwgap_halua_pam250.out \
          $ORIGDIR/hahu_nwgap_halua_pam250.out
#
# Check copy of hahu_nwgap_halua_pam250.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 hahu_nwgap_halua_pam250.out"
        echo " "
   else
        test -f hahu_nwgap_halua_pam250.out
        if [ $? -eq 0 ]
           then
               echo "PROBLEM IN COPY OF hahu_nwgap_halua_pam250.out"
               pwd
               far mkdir $PID  
               far store hahu_nwgap_halua_pam250.out \
                    $PID/hahu_nwgap_halua_pam250.out
           else
               echo "The file hahu_nwgap_halua_pam250.out does not exist."
           fi
        echo " "
   fi
#
cd $ORIGDIR 
/bin/rm -rf $TMPDIR