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diff snpEff_download.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
children
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--- a/snpEff_download.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpEff_download.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -3,7 +3,7 @@
 	<requirements>
 		<requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
-	<command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
+	<command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
 	<inputs>
 		<param name="genomeVersion" type="select" label="Genome">
 			<options from_file="snpeffect_genomedb.loc">