diff snpEff.xml @ 3:3b0c657b852b

Fix command in snpEff.xml
author Jim Johnson <jj@umn.edu>
date Wed, 06 Feb 2013 07:05:27 -0600
parents c07c403fc470
children b26a1aff7f81
line wrap: on
line diff
--- 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)"/>