# HG changeset patch
# User davidvanzessen
# Date 1383906560 18000
# Node ID d26e8c208b5f5b58d9a6fb154ac1c39f9488e837
# Parent bdf048a0b414d189309da4ae347e746f91dc28d9
Uploaded
diff -r bdf048a0b414 -r d26e8c208b5f r_wrapper.sh
--- a/r_wrapper.sh Fri Nov 08 05:29:02 2013 -0500
+++ b/r_wrapper.sh Fri Nov 08 05:29:20 2013 -0500
@@ -1,5 +1,35 @@
#!/bin/bash
+echo $1
+echo $2
+echo $3
+
+inputFile=$1
+outputFile=$2
+outputDir=$3
dir="$(cd "$(dirname "$0")" && pwd)"
-Rscript --verbose $dir/RScript.r $1 "$2.png" 2>&1
-mv -f "$2.png" $2
+mkdir $3
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1
+echo "" >> $2
+echo "
" >> $2
+echo "
" >> $2
+echo "
" >> $2
+samples=`cat $outputDir/samples.txt`
+count=1
+echo "" >> $outputFile
+for sample in $samples; do
+ echo " | " >> $outputFile
+ echo "
$sample |
" >> $outputFile
+ echo "V-D Heatmap: | V-J Heatmap: | D-J Heatmap: |
" >> $outputFile
+ mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
+ echo " | " >> $outputFile
+ mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
+ echo " | " >> $outputFile
+ mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
+ echo " |
" >> $outputFile
+ count=$((count+1))
+done
+echo "
" >> $outputFile
+
+echo "" >> $2
+