diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile
index 675650e5ac59..512cb3b71723 100644
--- a/biology/gatk/Makefile
+++ b/biology/gatk/Makefile
@@ -31,7 +31,9 @@ NO_ARCH=	yes
 
 DEPS_CACHE_DIR=	${WRKDIR}
 
-TEST_ENV=	${MAKE_ENV} JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so"
+TEST_ENV=	${MAKE_ENV} \
+		JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \
+		GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar
 
 PLIST_FILES=	bin/${PORTNAME} \
 		${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar