# HG changeset patch
# User fubar
# Date 1380517605 14400
# Node ID e3fb8f296482f24fab64825df3bce6926d0db18a
# Parent  a1e35baae42a174a736d569152942d155e0b4b4b
Uploaded

diff -r a1e35baae42a -r e3fb8f296482 snpeff33/snpEff.xml
--- a/snpeff33/snpEff.xml	Mon Sep 30 00:59:41 2013 -0400
+++ b/snpeff33/snpEff.xml	Mon Sep 30 01:06:45 2013 -0400
@@ -64,13 +64,13 @@
         <requirement type="package" version="3.3">snpEff</requirement>
     </requirements>
     <command>
+#if str( $intervals ) != 'None':     ### fix this for multiple dataset input
+  ln -s $intervals tempIntervals.bed &&
+#end if
 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
 fi";
-#if str( $intervals ) != 'None':     ### fix this for multiple dataset input
-  ln -s $intervals tempIntervals.bed &&
-#end if
 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 
 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
   -spliceSiteSize $spliceSiteSize