Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

diff combined.sh @ 2:bb8d5c67c129 draft

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Uploaded
author davidvanzessen
date Fri, 22 Nov 2013 08:12:40 -0500
parents 9b2567a3ecc9
children ba2ef103d26e
line wrap: on
line diff
--- a/combined.sh	Wed Nov 20 10:07:25 2013 -0500
+++ b/combined.sh	Fri Nov 22 08:12:40 2013 -0500
@@ -1,11 +1,18 @@
 #!/bin/bash
 
+export IGDATA=/home/david/Galaxy/galaxy-dist/toolsheddependencies/igBlastn/1.0.0/davidvanzessen/igblast_human/1c64c977624e/ncbi-igblast-1.0.0/;
+
+clonalType=${@:(-3):1}
 html=${@:(-2):1}
 imageDir=${@:(-1):1}
 dir="$(cd "$(dirname "$0")" && pwd)"
-fileCount=`expr $# - 2`
+fileCount=`expr $# - 3`
 array=("$@")
 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
+for var in "$@"
+do
+	echo "$var" >> $html
+done
 echo "<tr><td>-----------------------------------</td></tr>" >> $html
 limit=`expr $fileCount / 2`
 
@@ -57,7 +64,7 @@
 outputFile=$html
 outputDir=$imageDir
 mkdir $outputDir
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir 2>&1
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
 echo "<html>" > $outputFile
 echo "<img src='VPlot.png'/>" >> $outputFile
 echo "<img src='DPlot.png'/>" >> $outputFile
@@ -79,10 +86,6 @@
 	count=$((count+1))
 done
 echo "</table>" >> $outputFile
+echo "<h1>$clonalType</h1>" >> $outputFile
 
 echo "</html>" >> $2
-
-
-#r_wrapper.sh $in_file $out_file $out_file.files_path
-
-echo "<tr><td>done</td></tr>" >> $html