Mercurial > repos > fubar > snpeff_3_3_wrapper

comparison snpeff33/snpEff.xml @ 2:e3fb8f296482 draft

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Uploaded
author fubar
date Mon, 30 Sep 2013 01:06:45 -0400
parents a1e35baae42a
children 27194ef332fb
comparison
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1:a1e35baae42a 2:e3fb8f296482
62 --> 62 -->
63 <requirements> 63 <requirements>
64 <requirement type="package" version="3.3">snpEff</requirement> 64 <requirement type="package" version="3.3">snpEff</requirement>
65 </requirements> 65 </requirements>
66 <command> 66 <command>
67 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
68 ln -s $intervals tempIntervals.bed &&
69 #end if
67 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; 70 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
68 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; 71 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 ; 72 then java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion ;
70 fi"; 73 fi";
71 #if str( $intervals ) != 'None': ### fix this for multiple dataset input
72 ln -s $intervals tempIntervals.bed &&
73 #end if
74 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength 74 java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength
75 #if $spliceSiteSize and $spliceSiteSize.__str__ != '': 75 #if $spliceSiteSize and $spliceSiteSize.__str__ != '':
76 -spliceSiteSize $spliceSiteSize 76 -spliceSiteSize $spliceSiteSize
77 #end if 77 #end if
78 #if $filterIn and $filterIn.__str__ != 'no_filter': 78 #if $filterIn and $filterIn.__str__ != 'no_filter':