diff mutspecAnnot_wrapper.sh @ 7:eda59b985b1c draft default tip

Uploaded

--- a/mutspecAnnot_wrapper.sh	Tue Jun 28 02:59:32 2016 -0400
+++ b/mutspecAnnot_wrapper.sh	Mon Mar 13 08:21:19 2017 -0400
@@ -1,26 +1,29 @@
-#!/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
-
+#!/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" \
+	$*
+
+ls out/Mutational_Analysis/Annovar/
+
+if [ -e "out/Mutational_Analysis/Annovar/${name}.${refg}_multianno.txt" ]; then
+	cp out/Mutational_Analysis/Annovar/${name}.${refg}_multianno.txt $output
+fi
+
+exit 0
+