diff mutspecAnnot_wrapper.sh @ 0:8c682b3a7c5b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutspecAnnot_wrapper.sh	Tue Apr 19 03:07:11 2016 -0400
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+output=$1;shift
+refg=$2
+input=${9}
+
+command -v table_annovar.pl >/dev/null 2>&1 || {
+      echo "ERROR : table_annovar.pl not found. Add annovar scripts to your galaxy path !" ;
+      return 1 ;
+}
+
+mkdir out
+name=${input##*/}
+name=${name%%.*}
+
+perl $SCRIPT_PATH/mutspecAnnot.pl \
+	--outfile out \
+	--pathAVDBList $SCRIPT_PATH \
+	--temp "./temp" \
+	$* 2>&1
+
+ls out/Mutational_Analysis/Annovar/
+cp out/Mutational_Analysis/Annovar/${name}.${refg}_multianno.txt $output
+
+exit 0
+