diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile
index c8e8578e92f7..602b6f949228 100644
--- a/biology/samtools/Makefile
+++ b/biology/samtools/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	samtools
-PORTVERSION=	1.6
+DISTVERSION=	1.9
 CATEGORIES=	biology
 
 MAINTAINER=	cartwright@asu.edu
@@ -15,17 +15,16 @@ BUILD_DEPENDS=	htslib>=1.6:biology/htslib
 LIB_DEPENDS=	libhts.so:biology/htslib
 TEST_DEPENDS=	bash:shells/bash
 
+USES=		autoreconf gmake localbase ncurses \
+		perl5 python:env shebangfix
+
 USE_GITHUB=	yes
 
-USES=		autoreconf gmake ncurses perl5 python:env shebangfix
 USE_PERL5=	test
 GNU_CONFIGURE=	yes
 SUB_FILES=	pkg-message
 SHEBANG_FILES=	misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
 
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
-
 TEST_TARGET=	test
 
 .include <bsd.port.mk>
diff --git a/biology/samtools/distinfo b/biology/samtools/distinfo
index a0736b452989..fd46c27855ef 100644
--- a/biology/samtools/distinfo
+++ b/biology/samtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1508304738
-SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28
-SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195
+TIMESTAMP = 1532906637
+SHA256 (samtools-samtools-1.9_GH0.tar.gz) = 211600bd180d01030b3fe25baa7ae1c105106bed6c3f8d993f41dd278d44c637
+SIZE (samtools-samtools-1.9_GH0.tar.gz) = 4098992