diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile
index 5d4fa1eb9df6..35f30e18f80d 100644
--- a/biology/ucsc-userapps/Makefile
+++ b/biology/ucsc-userapps/Makefile
@@ -1,71 +1,71 @@
 PORTNAME=	ucsc-userapps
-DISTVERSION=	472
+DISTVERSION=	474
 CATEGORIES=	biology perl5 python
-MASTER_SITES=	http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
+MASTER_SITES=	https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
 DISTNAME=	userApps.v${DISTVERSION}.src
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Command line tools from the UCSC Genome Browser project
 WWW=		https://hgdownload.cse.ucsc.edu/admin/exe/
 
-# Some tools in the source dist are non-free for commercial use.
-# If they are added, the license below must be changed and packaging forbidden.
+# Note: Some tools in the source dist are non-free for commercial use.
+# If they are added to the install, the license below must be changed
+# and packaging forbidden.
 LICENSE=	MIT
 
 BUILD_DEPENDS=	bash:shells/bash
+# FIXME: Switch from mysql to mariadb
 LIB_DEPENDS=	libmysqlclient.so:databases/mysql80-client \
 		libunwind.so:devel/libunwind \
 		libfreetype.so:print/freetype2 \
 		libpng.so:graphics/png
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		gmake iconv localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz
 
-RESTRICTED=	Redistribution is limited, see license
-
 SHEBANG_FILES=	kent/src/checkUmask.sh \
 		kent/src/utils/bigHeat \
 		kent/src/utils/chromToUcsc/chromToUcsc \
 		kent/src/utils/tdbRename \
 		kent/src/utils/tdbSort \
 		kent/src/utils/trackDbIndexBb/trackDbIndexBb \
 		kent/src/utils/ucscApiClient \
 		kent/src/utils/webSync \
 		kent/src/utils/bigGuessDb/bigGuessDb
 
 WRKSRC=		${WRKDIR}/userApps
 CFLAGS+=	-fcommon
 MAKEFILE=	[Mm]akefile
 MAKE_ENV=	BINDIR=${WRKSRC}/bin
 
 SUB_FILES=	ucsc-shell
 
 # Build mostly non-commercial tools.  There is some leakage of proprietary
 # code from the libraries per conversation with UCSC.  Work to resolve this
 # is ongoing.
 do-build:
 	@(test -f ${WRKSRC}/kent/src/inc/my_uuid.h || ${MV} ${WRKSRC}/kent/src/inc/uuid.h ${WRKSRC}/kent/src/inc/my_uuid.h)
 	@${MKDIR} ${WRKSRC}/bin
 	@(cd ${WRKSRC}/kent/src/lib && ${DO_MAKE_BUILD})
 	@(cd ${WRKSRC}/kent/src/htslib && ${DO_MAKE_BUILD})
 	@(cd ${WRKSRC}/kent/src/jkOwnLib && ${DO_MAKE_BUILD})
 	@(cd ${WRKSRC}/kent/src/hg/lib && ${DO_MAKE_BUILD})
 	@(cd ${WRKSRC}/kent/src/utils && ${DO_MAKE_BUILD})
 	${CC} -DUCSC_PREFIX="\"${PREFIX}/userapps\"" ${FILESDIR}/kent.c -o ${WRKDIR}/kent
 
 do-install:
 	@${MKDIR} ${WRKSRC}/scripts ${WRKSRC}/binaries
 	@${CP} $$(file ${WRKSRC}/bin/* | fgrep ELF | cut -d : -f 1) \
 		${WRKSRC}/binaries
 	@${CP} $$(file ${WRKSRC}/bin/* | fgrep -v ELF | cut -d : -f 1) \
 		${WRKSRC}/scripts
 	@${MKDIR} ${STAGEDIR}${PREFIX}/userapps/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/binaries/* \
 		${STAGEDIR}${PREFIX}/userapps/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/* \
 		${STAGEDIR}${PREFIX}/userapps/bin
 	${INSTALL_SCRIPT} ${WRKDIR}/ucsc-shell \
 		${STAGEDIR}${PREFIX}/bin
 	${INSTALL_PROGRAM} ${WRKDIR}/kent ${STAGEDIR}${LOCALBASE}/bin
 
 .include <bsd.port.mk>
diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo
index e5f22b962d6f..ea61209e348b 100644
--- a/biology/ucsc-userapps/distinfo
+++ b/biology/ucsc-userapps/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1730984296
-SHA256 (userApps.v472.src.tgz) = 26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2
-SIZE (userApps.v472.src.tgz) = 24378966
+TIMESTAMP = 1732796640
+SHA256 (userApps.v474.src.tgz) = 87c465169b1246c3d2f56ea415461b7b2a4fb24bf5b7b95a3b590274cc7daec7
+SIZE (userApps.v474.src.tgz) = 24402279
diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c
deleted file mode 100644
index e75057e7937c..000000000000
--- a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c
+++ /dev/null
@@ -1,14 +0,0 @@
---- kent/src/hg/lib/jksql.c.orig	2024-10-16 04:15:27 UTC
-+++ kent/src/hg/lib/jksql.c
-@@ -1128,8 +1128,9 @@ if (sp->verifyServerCert && !sameString(sp->verifyServ
- // If turned on this can defeat Man-In-The-Middle attacks.
- if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0"))
-     {
--    #if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000
--    mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED);
-+    #if !defined(MARIADB_BASE_VERSION) && defined(MYSQL_VERSION_ID) && (MYSQL_VERSION_ID >= 80000)
-+    int ssl_mode = SSL_MODE_REQUIRED;
-+    mysql_options(conn, MYSQL_OPT_SSL_MODE, &ssl_mode);
-     #else
-     my_bool flag = TRUE;
-     mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag);