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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
1 <tool id="snpEff_download" name="SnpEff Download" version="3.2"> 1 <tool id="snpEff_download" name="SnpEff Download" version="3.2">
2 <description>Download a new database</description> 2 <description>Download a new database</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.2">snpEff</requirement> 4 <requirement type="package" version="3.2">snpEff</requirement>
5 </requirements> 5 </requirements>
6 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> 6 <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
7 <inputs> 7 <inputs>
8 <param name="genomeVersion" type="select" label="Genome"> 8 <param name="genomeVersion" type="select" label="Genome">
9 <options from_file="snpeffect_genomedb.loc"> 9 <options from_file="snpeffect_genomedb.loc">
10 <column name="name" index="1"/> 10 <column name="name" index="1"/>
11 <column name="value" index="0"/> 11 <column name="value" index="0"/>