Mercurial > repos > jjohnson > snpeff
comparison 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 |
comparison
equal
deleted
inserted
replaced
| 8:13b6ad2ddace | 9:937367efb1da |
|---|---|
| 62 --> | 62 --> |
| 63 <requirements> | 63 <requirements> |
| 64 <requirement type="package" version="3.2">snpEff</requirement> | 64 <requirement type="package" version="3.2">snpEff</requirement> |
| 65 </requirements> | 65 </requirements> |
| 66 <command> | 66 <command> |
| 67 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; | 67 SNPEFF_DATA_DIR=`grep '^data_dir' \$SNPEFF_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; |
| 68 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; | 68 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; |
| 69 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ; | 69 then java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion ; |
| 70 fi"; | 70 fi"; |
| 71 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength | 71 java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength |
| 72 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': | 72 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': |
| 73 -spliceSiteSize $spliceSiteSize | 73 -spliceSiteSize $spliceSiteSize |
| 74 #end if | 74 #end if |
| 75 #if $filterIn and $filterIn.__str__ != 'no_filter': | 75 #if $filterIn and $filterIn.__str__ != 'no_filter': |
| 76 -$filterIn | 76 -$filterIn |