diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index c2d33ef3ce82..ee2b20397ca6 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,58 +1,50 @@
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
 DISTVERSION=		0.51.1
+PORTREVISION=		1
 PORTEPOCH=		1
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Quantify abundances of transcripts from RNA-Seq data
 WWW=		https://pachterlab.github.io/kallisto/about.html
 
 LICENSE=	BSD2CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
 ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64 powerpc64le riscv64
 ONLY_FOR_ARCHS_REASON=	Requires a 64-bit processor
 
 LIB_DEPENDS=	libhdf5.so:science/hdf5 \
 		libsz.so:science/libaec \
 		libhts.so:biology/htslib
 
 USES=		cmake:noninja compiler:c++11-lang gmake localbase:ldflags
 USE_GITHUB=	yes
 GH_ACCOUNT=	pachterlab
 
 EXTRACT_AFTER_ARGS=	--exclude ${GH_PROJECT_DEFAULT}-${GH_TAGNAME_EXTRACT}/ext/htslib --no-same-owner --no-same-permissions
 
 SUB_FILES=	kallisto-test
 
 PORTEXAMPLES=		*
 PLIST_FILES=		bin/kallisto
 EXAMPLES_PLIST_FILES=	bin/kallisto-test
 
 # hdf5 is being phased out and is no longer built in by default, but is still
 # required for Sleuth (requires kallisto bootstrap estimates) and other
 # downstream tools.  Remove this after Sleuth et al catch up.
 CMAKE_ARGS+=		-DUSE_HDF5:BOOL=ON -DUSE_BAM:BOOL=ON
 # WIP: Remove before committing
 CMAKE_ARGS+=		-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 MAKE_JOBS_UNSAFE=	yes
 CXXFLAGS+=		-Wno-unqualified-std-cast-call
 LDFLAGS+=		-lhts -lz
 
 OPTIONS_DEFINE=	EXAMPLES
 
-.include <bsd.port.pre.mk>
-
-# Build fails with clang19, but succeeds with gcc13
-# Have not figured out where this sz_link member is even supposed to come from
-# DataStorage.tcc:81:69: error: no member named 'sz_link' in 'DataStorage<Unitig_data_t>'
-.if ${OSVERSION} > 1500000
-USE_GCC=	yes
-.endif
-
 post-install-EXAMPLES-on:
 	${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index 98b8775d9539..a207db3e922d 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1726658334
+TIMESTAMP = 1748283025
 SHA256 (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516
 SIZE (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = 5954250
diff --git a/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc b/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc
new file mode 100644
index 000000000000..0e6dcb8cca18
--- /dev/null
+++ b/biology/kallisto/files/patch-ext_bifrost_src_DataStorage.tcc
@@ -0,0 +1,14 @@
+--- ext/bifrost/src/DataStorage.tcc.orig	2024-09-17 05:40:08 UTC
++++ ext/bifrost/src/DataStorage.tcc
+@@ -78,7 +78,10 @@ DataStorage<U>::DataStorage(const DataStorage& o) : co
+ 
+         unitig_cs_link = new atomic<uint64_t>[sz_link];
+ 
+-        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.sz_link[i].load();
++        // Hayzam Sherif: o.sz_link -> o.unitig_cs_link
++        // Independently proposed by Lucas van Dijk:
++        // https://github.com/pmelsted/bifrost/pull/18/files
++        for (size_t i = 0; i != sz_link; ++i) unitig_cs_link[i] = o.unitig_cs_link[i].load();
+     }
+ 
+     if ((o.data != nullptr) && (o.sz_cs != 0)){