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diff snpSift_int.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/snpSift_int.xml	Mon May 13 12:45:07 2013 -0500
+++ b/snpSift_int.xml	Wed Sep 18 10:49:56 2013 -0500
@@ -8,7 +8,7 @@
                 <requirement type="package" version="3.2">snpEff</requirement>
 	</requirements>
 	<command>
-		java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+		java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
 	</command>
 	<inputs>
 		<param format="vcf" name="input" type="data" label="VCF input"/>