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

set -x
ORIGDIR=`pwd`
PID=$$
export PID
TMPDIR=/scratch/$USER/$PID
export TMPDIR
mkdir -p $TMPDIR
cd $TMPDIR
#
# Copy: $ORIGDIR/f1k.nbrf
# to: f1k.nbrf
#
cp $ORIGDIR/f1k.nbrf f1k.nbrf
#
# Copy: $ORIGDIR/plbo.nbrf
# to: plbo.nbrf
#
cp $ORIGDIR/plbo.nbrf plbo.nbrf
#
#
# Run program    maxsegs with the input coming
# From the following *HERE* Document.
# (NOTE: This is shell specific!)
#
/biomed/bin/maxsegs <<\EOF
ECHO
TITLE Finding kringles in plbo.
SEQUENCE QUERY=f1k.nbrf
SEQUENCE LIBRARY=plbo.nbrf
SEQUENCE RESULT=f1-k_maxsegs_plbo_pam40.srt
ALPHABET PROTEIN
SCORE PAM40
LIMIT NUMBER=6 cutoff=0
SHOW
MATCH
QUIT
EOF
#
# This is the end of the input file.

#        echo " "
ls -la
#
/biomed/bin/seqsort -program maxsegs -in f1-k_maxsegs_plbo_pam40.srt \
                         -out f1-k_maxsegs_plbo_pam40.out \
                         -list f1-k_maxsegs_plbo_pam40.lst 
#
# Copy: f1-k_maxsegs_plbo_pam40.out
# to: $ORIGDIR/f1-k_maxsegs_plbo_pam40.out
#
cp f1-k_maxsegs_plbo_pam40.out \
          $ORIGDIR/f1-k_maxsegs_plbo_pam40.out
#
# Check copy of f1-k_maxsegs_plbo_pam40.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 f1-k_maxsegs_plbo_pam40.out"
        echo " "
   else
        test -f f1-k_maxsegs_plbo_pam40.out
        if [ $? -eq 0 ]
           then
               echo "PROBLEM IN COPY OF f1-k_maxsegs_plbo_pam40.out"
               pwd
               far mkdir $PID  
               far store f1-k_maxsegs_plbo_pam40.out \
                    $PID/f1-k_maxsegs_plbo_pam40.out
           else
               echo "The file f1-k_maxsegs_plbo_pam40.out does not exist."
           fi
        echo " "
   fi
#
#
# Copy: f1-k_maxsegs_plbo_pam40.lst
# to: $ORIGDIR/f1-k_maxsegs_plbo_pam40.lst
#
cp f1-k_maxsegs_plbo_pam40.lst \
          $ORIGDIR/f1-k_maxsegs_plbo_pam40.lst
#
# Check copy of f1-k_maxsegs_plbo_pam40.lst
# 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 f1-k_maxsegs_plbo_pam40.lst"
        echo " "
   else
        test -f f1-k_maxsegs_plbo_pam40.lst
        if [ $? -eq 0 ]
           then
               echo "PROBLEM IN COPY OF f1-k_maxsegs_plbo_pam40.lst"
               pwd
               far mkdir $PID  
               far store f1-k_maxsegs_plbo_pam40.lst \
                    $PID/f1-k_maxsegs_plbo_pam40.lst
           else
               echo "The file f1-k_maxsegs_plbo_pam40.lst does not exist."
           fi
        echo " "
   fi
#
cd $ORIGDIR 
/bin/rm -rf $TMPDIR