Mercurial > repos > jjohnson > snpeff
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 |
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--- 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)"/>