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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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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