diff mda_heatmap_gen/heatmap.sh @ 0:73aa1f80c237 draft

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mda_heatmap_gen/heatmap.sh	Thu Apr 07 10:54:23 2016 -0400
@@ -0,0 +1,30 @@
+echo $1 $2 $3 $4 $5 $6 $7 $8 $9 ${10} ${11} ${12} ${13} ${14} ${15}
+
+#create temp directory for row and col order and dendro files.
+tdir=${11}/$(date +%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 $tdir/CDfile.txt)"
+rc=$?; if [[ $rc != 0 ]]; then echo $output; exit $rc; fi
+
+
+#there are a variable number of triplicate parameters for classification bars
+count=0
+classifcations=''
+
+for i in "$@"; do
+  if [ $count -gt 10 ]
+  then
+    classifications=$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 Row Column $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