#! /bin/sh
#SLURM -N 1
#SLURM -t 5:00
#SLURM -o clustal.out

set -x

ORIGDIR=`pwd`
PID=$$
export PID
TMPDIR=/tmp/$USER/$PID
export TMPDIR
mkdir -p $TMPDIR
cd $TMPDIR
#
# Copy: $ORIGDIR/seq.pir
# to: seq.pir
#
cp $ORIGDIR/seq.pir seq.pir
#
srun /home/biomed/bin/clustalw <<EOF
1
seq.pir
2
9
3

1



x

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