diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile
index 4ae2b8bd94ec..8774208d9097 100644
--- a/biology/kallisto/Makefile
+++ b/biology/kallisto/Makefile
@@ -1,50 +1,49 @@
 PORTNAME=		kallisto
 DISTVERSIONPREFIX=	v
-DISTVERSION=		0.50.0
-PORTREVISION=		2
+DISTVERSION=		0.50.1
 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
 
 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
 LDFLAGS+=		-lhts -lz
 
 OPTIONS_DEFINE=	EXAMPLES
 
 post-extract:
 	${RM} -rf ${WRKSRC}/ext/htslib
 
 post-install-EXAMPLES-on:
 	${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/kallisto/distinfo b/biology/kallisto/distinfo
index e216bb4ae394..f01c0d8e6e1c 100644
--- a/biology/kallisto/distinfo
+++ b/biology/kallisto/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1688395958
-SHA256 (pachterlab-kallisto-v0.50.0_GH0.tar.gz) = f9cc0058d08206cb6dde4a4dcaf8a778df5a939a6e021508eea9b00b0d6d5368
-SIZE (pachterlab-kallisto-v0.50.0_GH0.tar.gz) = 5939018
+TIMESTAMP = 1698923323
+SHA256 (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 030752bab3b0e33cd3f23f6d8feddd74194e5513532ffbf23519e84db2a86d34
+SIZE (pachterlab-kallisto-v0.50.1_GH0.tar.gz) = 5947303
diff --git a/biology/kallisto/files/patch-src_main.cpp b/biology/kallisto/files/patch-src_main.cpp
new file mode 100644
index 000000000000..2eadc428781c
--- /dev/null
+++ b/biology/kallisto/files/patch-src_main.cpp
@@ -0,0 +1,10 @@
+--- src/main.cpp.orig	2023-11-02 11:38:09 UTC
++++ src/main.cpp
+@@ -11,6 +11,7 @@
+ #include <limits>
+ 
+ #include <cstdio>
++#include <unistd.h>	// rmdir()
+ 
+ #include "common.h"
+ #include "ProcessReads.h"