--- a/wrapper.sh	Tue Apr 07 07:32:43 2015 -0400
+++ b/wrapper.sh	Wed Apr 08 05:25:52 2015 -0400
@@ -15,13 +15,10 @@
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
 cat $PWD/files/*/10_* > $PWD/hotspots.txt
 
-BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
+#BLASTN_DIR="/home/galaxy/tmp/blast/ncbi-blast-2.2.30+/bin"
 
 echo "${BLASTN_DIR}"
 
-
-
-
 echo "identification ($method)"
 
 if [[ "${method}" == "custom" ]] ; then
@@ -50,6 +47,8 @@
 Rscript $dir/mutation_analysis.r $outdir/merged.txt $genes $outdir ${include_fr1} 2>&1
 echo "python mutation analysis"
 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --output $outdir/hotspot_analysis.txt
+echo "R AA histogram"
+Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1
 
 cat $outdir/mutations.txt $outdir/hotspot_analysis.txt > $outdir/result.txt
 
@@ -79,17 +78,26 @@
 
 
 echo "<img src='all.png'/><br />" >> $output
+echo "<a href='all.txt'>download data</a><br />" >> $output
 if [ -a $outdir/ca.png ] 
 then
 	echo "<img src='ca.png'/><br />" >> $output
+	echo "<a href='ca.txt'>download data</a><br />" >> $output
 fi
 if [ -a $outdir/cg.png ]
 then
 	echo "<img src='cg.png'/><br />" >> $output
+	echo "<a href='cg.txt'>download data</a><br />" >> $output
 fi
 if [ -a $outdir/scatter.png ]
 then
 	echo "<img src='scatter.png'/><br />" >> $output
+	echo "<a href='scatter.txt'>download data</a><br />" >> $output
+fi
+if [ -a $outdir/aa_histogram.png ]
+then
+	echo "<img src='aa_histogram.png'/><br />" >> $output
+	echo "<a href='aa_histogram.txt'>download data</a><br />" >> $output
 fi
 
 for gene in ${genes[@]}