echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17}
#create temp directory for row and col order and dendro files.
tdir=${11}/$(date +%y%m%d%M%S)
echo $tdir
mkdir $tdir
#run R to cluster matrix
output="$(R --slave --vanilla --file=${11}/CHM.R --args $3 $4 $5 $6 $7 $8 $9 $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${12} ${13} ${14} ${15} 2>&1)"
rc=$?;
if [ $rc != 0 ]
then
  echo $output;
  if [ `echo "$output" | grep -c "Inf in foreign function call"` -gt 0 ]
  then
    echo "";
    echo "Note: This error can occur when there is no variation in a row or column.  Try a different distance measure or remove rows/columns without variation.";
  fi
  exit $rc;
fi

#there are a variable number of triplicate parameters for classification bars
count=0
classifications=''

#if row cut was done, add that autogenerated classification
if [ ${12} -gt 1 ]
then
  classifications="Class $tdir/ROfile.txt.cut row_categorical"
fi

#if col cut was done, add that autogenerated classification
if [ ${13} -gt 1 ]
then
  classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
fi

#now add the user provided classification files 
for i in "$@"; do
  if [ $count -gt 14 ]
  then
    classifications=$classifications' '$i
  fi
  count=$((count+1))
done
#call java program to generate NGCHM viewer files.
java -jar ${11}/GalaxyMapGen.jar "${1}" "${2}" DataLayer1 $3 linear ${14} ${15} $4 $5 $6 $tdir/ROfile.txt $tdir/RDfile.txt $7 $8 $9 $tdir/COfile.txt $tdir/CDfile.txt ${10} $classifications
#clean up tempdir
rm -rf $tdir