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comparison snpSift_annotate.xml @ 9:937367efb1da default tip

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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
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8:13b6ad2ddace 9:937367efb1da
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.2">snpEff</requirement> 8 <requirement type="package" version="3.2">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar $annotate_cmd 11 java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd
12 #if $annotate.id : 12 #if $annotate.id :
13 -id 13 -id
14 #elif $annotate.info_ids.__str__.strip() != '' : 14 #elif $annotate.info_ids.__str__.strip() != '' :
15 -info "$annotate.info_ids" 15 -info "$annotate.info_ids"
16 #end if 16 #end if