--- a/heatmap.sh	Thu Jul 20 15:31:06 2017 -0400
+++ b/heatmap.sh	Tue Dec 05 14:57:34 2017 -0500
@@ -1,23 +1,12 @@
-echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17}
-
-#run python to validate the input matrix and covariate files (if any)
-#output="$(python  ${11}/mda_heatmap_gen.py $@)"
-output=$(python  ${11}/mda_heatmap_gen.py "$@")
-rc=$?;
-echo $output;
-if [ $rc != 0 ]
-then
-  exit $rc;
-fi
-
+#echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15} ${16} ${17} ${18}
 
 #create temp directory for row and col order and dendro files.
-tdir=${11}/$(date +%y%m%d%M%S)
+tdir=${12}/$(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} ${15} 2>&1)"
+output="$(R --slave --vanilla --file=${12}/CHM.R --args $4 $5 $6 $7 $8 $9 ${10} $tdir/ROfile.txt $tdir/COfile.txt $tdir/RDfile.txt $tdir/CDfile.txt ${13} ${14} ${15} ${16} 2>&1)"
 rc=$?;
 if [ $rc != 0 ]
 then
@@ -26,6 +15,7 @@
   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.";
+    echo "This error may also be caused when a covariate file has inadvertently been selected as an Input Matrix.  Check your Input Matrix entry.";
   fi
   exit $rc;
 fi
@@ -35,26 +25,28 @@
 classifications=''
 
 #if row cut was done, add that autogenerated classification
-if [ ${12} -gt 1 ]
+if [ ${13} -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 ]
+if [ ${14} -gt 1 ]
 then
   classifications="$classifications Class $tdir/COfile.txt.cut col_categorical"
 fi
 
 #now add the user provided classification files 
 for i in "$@"; do
-  if [ $count -gt 14 ]
+  if [ $count -gt 16 ]
   then
     classifications=$classifications' '$i
   fi
   count=$((count+1))
 done
+echo "classifications " $classifications
+echo "${11} " ${11}
 #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
+java -jar ${12}/GalaxyMapGen.jar "${1}" "${2}" "${3}" DataLayer1 $4 linear ${15} ${16} $5 $6 $7 $tdir/ROfile.txt $tdir/RDfile.txt $8 $9 ${10} $tdir/COfile.txt $tdir/CDfile.txt ${11} $classifications
 #clean up tempdir
 rm -rf $tdir