Mercurial > repos > jjohnson > snpeff_with_dep

diff snpEff.xml @ 17:aab5e0adb26d

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Remove environment requirement
author Jim Johnson <jj@umn.edu>
date Fri, 21 Sep 2012 18:23:28 -0500
parents ef4598ea7179
children 1cae7fb31da7
line wrap: on
line diff
--- a/snpEff.xml	Fri Sep 21 16:20:13 2012 -0500
+++ b/snpEff.xml	Fri Sep 21 18:23:28 2012 -0500
@@ -7,7 +7,6 @@
 	-->
 	<requirements>
 		<requirement type="package" version="3.0">snpEff</requirement>
-		<requirement type="set_environment">JAVA_JAR_PATH </requirement>
 	</requirements>
 	<command>java -Xmx6G -jar \$JAVA_JAR_PATH/snpEff.jar eff -c \$JAVA_JAR_PATH/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command>
 	<inputs>