# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1360155927 21600
# Node ID 3b0c657b852b1abe5b57dba6654ab8938beb6ff3
# Parent  a9bae7957c361e767f9c57146e16cd9e5d15ff46
Fix command in snpEff.xml

diff -r a9bae7957c36 -r 3b0c657b852b snpEff.xml
--- a/snpEff.xml	Wed Jan 30 17:29:10 2013 -0600
+++ b/snpEff.xml	Wed Feb 06 07:05:27 2013 -0600
@@ -9,10 +9,10 @@
 		<requirement type="package" version="3.1">snpEff</requirement>
 	</requirements>
 	<command>
-export SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
-if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
+SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
+eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download  -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
-fi;
+fi";
 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
 	<inputs>
 		<param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/>