Mercurial > repos > fubar > snpeff_3_3_wrapper

comparison snpeff33/snpEff.xml @ 3:27194ef332fb draft default tip

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Uploaded
author fubar
date Mon, 30 Sep 2013 01:13:52 -0400
parents e3fb8f296482
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2:e3fb8f296482 3:27194ef332fb
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 67 #if str( $intervals ) != 'None':
68 ln -s $intervals tempIntervals.bed && 68 ln -s $intervals tempIntervals.bed &amp;&amp;
69 #end if 69 #end if
70 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`; 70 SNPEFF_DATA_DIR=`grep '^data_dir' \$JAVA_JAR_PATH/snpEff.config | sed 's/.*data_dir.*[=:]//'`;
71 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ; 71 eval "if [ ! -e \$SNPEFF_DATA_DIR/$genomeVersion ] ;
72 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 ;
73 fi"; 73 fi";