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comparison snpSift_annotate.xml @ 1:ebe280eca4a4

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Add package requirement
author Jim Johnson <jj@umn.edu>
date Thu, 13 Sep 2012 21:40:44 -0500
parents 388f178f9e13
children c641d515de2e
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0:388f178f9e13 1:ebe280eca4a4
3 <!-- 3 <!--
4 You will need to change the path to wherever your installation is. 4 You will need to change the path to wherever your installation is.
5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.0f">snpEff</requirement>
8 <requirement type="set_environment">JAVA_JAR_PATH </requirement> 9 <requirement type="set_environment">JAVA_JAR_PATH </requirement>
9 </requirements> 10 </requirements>
10 <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command> 11 <command>java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar annotate -q $dbSnp $input > $output </command>
11 <inputs> 12 <inputs>
12 <param format="vcf" name="input" type="data" label="VCF input"/> 13 <param format="vcf" name="input" type="data" label="VCF input"/>