Index: head/biology/kallisto/Makefile
===================================================================
--- head/biology/kallisto/Makefile	(revision 526243)
+++ head/biology/kallisto/Makefile	(revision 526244)
@@ -1,35 +1,39 @@
 # $FreeBSD$
 
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
-DISTVERSION=		0.46.1
+DISTVERSION=		0.46.2
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Quantify abundances of transcripts from RNA-Seq data
 
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
 LIB_DEPENDS=	libhdf5.so:science/hdf5 \
 		libsz.so:science/szip \
 		libhts.so:biology/htslib
 
-USES=		cmake:noninja compiler:c++11-lang
+USES=		cmake:noninja compiler:c++11-lang localbase:ldflags
 USE_GITHUB=	yes
 GH_ACCOUNT=	pachterlab
 
 SUB_FILES=	kallisto-test
 
 PORTEXAMPLES=		*
 PLIST_FILES=		bin/kallisto
 EXAMPLES_PLIST_FILES=	bin/kallisto-test
 
+# hdf5 is being phased out and is no longer build in by default, but is still
+# required for Sleuth and other downstream tools.  Remove this after Sleuth
+# et all catch up.
+CMAKE_ARGS+=	-DUSE_HDF5:BOOL=ON
+
 OPTIONS_DEFINE=	EXAMPLES
-LDFLAGS+=	-L${LOCALBASE}/lib
 
 post-install-EXAMPLES-on:
 	${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
Index: head/biology/kallisto/distinfo
===================================================================
--- head/biology/kallisto/distinfo	(revision 526243)
+++ head/biology/kallisto/distinfo	(revision 526244)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1572972210
-SHA256 (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 492ef081395e8858fcd9832aceb8b61c79358f00afb45e6709146c0fb51dd231
-SIZE (pachterlab-kallisto-v0.46.1_GH0.tar.gz) = 2254560
+TIMESTAMP = 1581611719
+SHA256 (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 10bab0c2929d8c345750e02735b305bbbfa89e8a48f42c4b9af44f3d44ff4c82
+SIZE (pachterlab-kallisto-v0.46.2_GH0.tar.gz) = 2693857