--- a/wrapper.sh	Fri Mar 25 04:39:18 2016 -0400
+++ b/wrapper.sh	Fri Mar 25 07:50:12 2016 -0400
@@ -14,7 +14,7 @@
 mkdir $outdir
 
 echo "---------------- read parameters ----------------"
-echo "---------------- read parameters ----------------" > $output
+echo "---------------- read parameters ----------------<br />" > $output
 
 echo "unpacking IMGT file"
 
@@ -43,7 +43,7 @@
 echo "${BLASTN_DIR}"
 
 echo "identification ($method)"
-echo "identification ($method)" >> $output
+echo "identification ($method)<br />" >> $output
 
 echo "blast or custom"
 
@@ -66,12 +66,12 @@
 fi
 
 echo "---------------- merge_and_filter.r ----------------"
-echo "---------------- merge_and_filter.r ----------------" >> $output
+echo "---------------- merge_and_filter.r ----------------<br />" >> $output
 
 Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique}
 
 echo "---------------- mutation_analysis.r ----------------"
-echo "---------------- mutation_analysis.r ----------------" >> $output
+echo "---------------- mutation_analysis.r ----------------<br />" >> $output
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"
@@ -83,13 +83,13 @@
 
 
 echo "---------------- mutation_analysis.py ----------------"
-echo "---------------- mutation_analysis.py ----------------" >> $output
+echo "---------------- mutation_analysis.py ----------------<br />" >> $output
 
 python $dir/mutation_analysis.py --input $outdir/merged.txt --genes $genes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
 echo "R AA histogram"
 
 echo "---------------- aa_histogram.r ----------------"
-echo "---------------- aa_histogram.r ----------------" >> $output
+echo "---------------- aa_histogram.r ----------------<br />" >> $output
 
 Rscript $dir/aa_histogram.r $outdir/aa_mutations.txt $outdir/aa_histogram.png 2>&1