Mercurial > repos > jjohnson > snpeff
diff snpEff.xml @ 9:937367efb1da default tip
Change tool dependency to package_snpeff_3_2, now uses environment variable: SNPEFF_JAR_PATH for the location of snpeff jar files.
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 18 Sep 2013 10:49:56 -0500 |
| parents | 13b6ad2ddace |
| children |
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--- a/snpEff.xml Mon May 13 12:45:07 2013 -0500 +++ b/snpEff.xml Wed Sep 18 10:49:56 2013 -0500 @@ -64,11 +64,11 @@ <requirement type="package" version="3.2">snpEff</requirement> </requirements> <command> -SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; +SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_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 ; +then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ; fi"; -java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength +java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength #if $spliceSiteSize and $spliceSiteSize.__str__ != '': -spliceSiteSize $spliceSiteSize #end if