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view snpEff_2_1a/scripts/snpSift.sh @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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#!/bin/sh

DIR=$HOME/snpEff/
DIR_SNPSIFT=$HOME/snpEff/snpSiftBin/
LIB=$HOME/snpEff/lib
LIB_SNPSIFT=$HOME/snpEff/snpSiftLib/

# Old library reference:
#	-classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR:$DIR_SNPSIFT" \

java -Xmx1G \
	-classpath "$LIB/charts4j-1.2.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$LIB_SNPSIFT/antlr-3.4-complete.jar:$DIR:$DIR_SNPSIFT" \
	ca.mcgill.mcb.pcingola.vcfEtc.SnpSift \
	$*