diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile
index 3621160d0594..7ed02e4b69ce 100644
--- a/biology/ucsc-userapps/Makefile
+++ b/biology/ucsc-userapps/Makefile
@@ -1,76 +1,78 @@
 PORTNAME=	ucsc-userapps
-DISTVERSION=	414
-PORTREVISION=	1
+DISTVERSION=	472
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/
-DISTNAME=	userApps.v${PORTVERSION}.src
+DISTNAME=	userApps.v${DISTVERSION}.src
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Command line tools from the UCSC Genome Browser project
 WWW=		https://hgdownload.cse.ucsc.edu/admin/exe/
 
 LICENSE=	UCSC-GB
 LICENSE_NAME=	UCSC Genome Browser License
 LICENSE_TEXT=	Some tools installed by this port require a license for\
 		commercial use.\n\nContact UCSC directly if you are using\
 		these tools for commercial purposes.\n\nSee\
 		https://genome.ucsc.edu/license/ for full terms.
 LICENSE_PERMS=	no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell
 
 ONLY_FOR_ARCHS=		amd64
 ONLY_FOR_ARCHS_REASON=	uses _mm_popcnt_u64() function
 
 BUILD_DEPENDS=	bash:shells/bash
-LIB_DEPENDS=	libiconv.so:converters/libiconv \
+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 localbase:ldflags mysql shebangfix perl5 python ssl tar:tgz
+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/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:
-	@${MV} ${WRKSRC}/kent/src/inc/uuid.h ${WRKSRC}/kent/src/inc/my_uuid.h
+	@(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 cc2c9ed9a4e7..e5f22b962d6f 100644
--- a/biology/ucsc-userapps/distinfo
+++ b/biology/ucsc-userapps/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1621027743
-SHA256 (userApps.v414.src.tgz) = 36910b5c84ea613d4eb6ccb9572f3b34d929c5571578b1d91013391895638ab0
-SIZE (userApps.v414.src.tgz) = 19195157
+TIMESTAMP = 1730984296
+SHA256 (userApps.v472.src.tgz) = 26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2
+SIZE (userApps.v472.src.tgz) = 24378966
diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c
index f97872c005d2..9f2b33c711da 100644
--- a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c
+++ b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_eap_eapFinish_eapFinish.c
@@ -1,11 +1,11 @@
---- kent/src/hg/encode3/eap/eapFinish/eapFinish.c.orig	2021-04-14 11:23:30 UTC
+--- kent/src/hg/encode3/eap/eapFinish/eapFinish.c.orig	2024-10-16 04:15:27 UTC
 +++ kent/src/hg/encode3/eap/eapFinish/eapFinish.c
 @@ -3,7 +3,7 @@
  
  /* Copyright (C) 2014 The Regents of the University of California 
-  * See README in this or parent directory for licensing information. */
+  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 -#include <uuid/uuid.h>
 +#include <uuid.h>
  #include "common.h"
  #include "linefile.h"
  #include "hash.h"
diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c
index cdd532d146eb..8c40a258cf40 100644
--- a/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c
+++ b/biology/ucsc-userapps/files/patch-kent_src_hg_encode3_encodeDataWarehouse_edwWebRegisterScript_edwWebRegisterScript.c
@@ -1,11 +1,11 @@
---- kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c.orig	2021-04-14 11:23:12 UTC
+--- kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c.orig	2024-10-16 04:15:27 UTC
 +++ kent/src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
 @@ -2,7 +2,7 @@
  
  /* Copyright (C) 2014 The Regents of the University of California 
-  * See README in this or parent directory for licensing information. */
+  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 -#include <uuid/uuid.h>
 +#include <uuid.h>
  #include "common.h"
  #include "linefile.h"
  #include "hash.h"
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
new file mode 100644
index 000000000000..e75057e7937c
--- /dev/null
+++ b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c
@@ -0,0 +1,14 @@
+--- 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);
diff --git a/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk b/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk
index b083cbf175c9..c04678ded9e1 100644
--- a/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk
+++ b/biology/ucsc-userapps/files/patch-kent_src_inc_common.mk
@@ -1,13 +1,12 @@
---- kent/src/inc/common.mk.orig	2021-04-02 22:47:03 UTC
+--- kent/src/inc/common.mk.orig	2024-10-16 04:15:27 UTC
 +++ kent/src/inc/common.mk
-@@ -61,6 +61,10 @@ else
+@@ -65,6 +65,9 @@ ifeq ($(UNAME_S),Darwin)
+   ifneq ($(wildcard /opt/local/lib/libiconv.a),)
+     ICONVLIB = /opt/local/lib/libiconv.a
+   endif
++  ifeq ($(UNAME_S),FreeBSD)
++    ICONVLIB=-L${LOCALBASE}/lib -liconv
++  endif
+   ifneq ($(wildcard /opt/homebrew/lib/libmysqlclient.a),)
+     MYSQLLIBS = /opt/homebrew/lib/libmysqlclient.a
    endif
- endif
- 
-+ifeq ($(UNAME_S),FreeBSD)
-+  ICONVLIB=-L${LOCALBASE}/lib -liconv
-+endif
-+
- # autodetect if openssl is installed
- ifeq (${SSLDIR},)
-   SSLDIR = /usr/include/openssl
diff --git a/biology/ucsc-userapps/files/ucsc-shell.in b/biology/ucsc-userapps/files/ucsc-shell.in
old mode 100755
new mode 100644
diff --git a/biology/ucsc-userapps/pkg-descr b/biology/ucsc-userapps/pkg-descr
index 05129f558f62..e3ad755eee45 100644
--- a/biology/ucsc-userapps/pkg-descr
+++ b/biology/ucsc-userapps/pkg-descr
@@ -1,6 +1,5 @@
 These are the command-line bioinformatics utilities associated with the UCSC
 genome browser.  Care has been taken to install only the freely available
 tools.  However, the license information at https://genome.ucsc.edu/license/
 is not entirely clear and we may add non-free utilities in the future.
-
 Contact UCSC if you are using this port for commercial purposes.
diff --git a/biology/ucsc-userapps/pkg-plist b/biology/ucsc-userapps/pkg-plist
index f8605fc771d0..52e1fcc7fc79 100644
--- a/biology/ucsc-userapps/pkg-plist
+++ b/biology/ucsc-userapps/pkg-plist
@@ -1,137 +1,155 @@
 bin/kent
 bin/ucsc-shell
 userapps/bin/aNotB
 userapps/bin/addCols
 userapps/bin/ave
 userapps/bin/aveCols
 userapps/bin/bamToPsl
+userapps/bin/barChartMaxLimit
 userapps/bin/bedClip
 userapps/bin/bedCommonRegions
 userapps/bin/bedGeneParts
 userapps/bin/bedGraphPack
 userapps/bin/bedGraphToBigWig
 userapps/bin/bedJoinTabOffset
+userapps/bin/bedJoinTabOffset.py
 userapps/bin/bedPileUps
 userapps/bin/bedRemoveOverlap
 userapps/bin/bedRestrictToPositions
 userapps/bin/bedToBigBed
 userapps/bin/bigBedInfo
 userapps/bin/bigBedNamedItems
 userapps/bin/bigBedSummary
 userapps/bin/bigBedToBed
+userapps/bin/bigGuessDb
+userapps/bin/bigHeat
 userapps/bin/bigWigAverageOverBed
 userapps/bin/bigWigCat
 userapps/bin/bigWigCluster
 userapps/bin/bigWigCorrelate
 userapps/bin/bigWigInfo
 userapps/bin/bigWigMerge
 userapps/bin/bigWigSummary
 userapps/bin/bigWigToBedGraph
 userapps/bin/bigWigToWig
 userapps/bin/calc
 userapps/bin/catDir
 userapps/bin/catUncomment
 userapps/bin/ccCp
 userapps/bin/chopFaLines
+userapps/bin/chromToUcsc
 userapps/bin/clusterMatrixToBarChartBed
 userapps/bin/colTransform
 userapps/bin/convolve
 userapps/bin/countChars
 userapps/bin/cpg_lh
 userapps/bin/detab
 userapps/bin/dnsInfo
 userapps/bin/endsInLf
+userapps/bin/expMatrixToBarchartBed
 userapps/bin/faAlign
 userapps/bin/faCmp
 userapps/bin/faCount
 userapps/bin/faFilter
 userapps/bin/faFilterN
 userapps/bin/faFlyBaseToUcsc
 userapps/bin/faFrag
 userapps/bin/faGapLocs
 userapps/bin/faGapSizes
 userapps/bin/faNcbiToUcsc
 userapps/bin/faNoise
 userapps/bin/faOneRecord
 userapps/bin/faPolyASizes
 userapps/bin/faRandomize
 userapps/bin/faRc
 userapps/bin/faRenameRecords
 userapps/bin/faSimplify
 userapps/bin/faSize
 userapps/bin/faSomeRecords
 userapps/bin/faSplit
 userapps/bin/faToFastq
 userapps/bin/faToNib
 userapps/bin/faToTab
 userapps/bin/faToTwoBit
 userapps/bin/faTrans
 userapps/bin/faTrimPolyA
 userapps/bin/faTrimRead
 userapps/bin/fastqStatsAndSubsample
 userapps/bin/fastqToFa
 userapps/bin/findMotif
 userapps/bin/fixCr
 userapps/bin/gapSplit
 userapps/bin/gffPeek
 userapps/bin/git-reports
 userapps/bin/gmtime
 userapps/bin/headRest
 userapps/bin/htmlCheck
 userapps/bin/htmlPics
 userapps/bin/jkUniq
 userapps/bin/lineCount
 userapps/bin/linesToRa
 userapps/bin/localtime
+userapps/bin/matrixClusterColumns
+userapps/bin/matrixMarketToTsv
+userapps/bin/matrixNormalize
+userapps/bin/matrixToBarChartBed
 userapps/bin/mktime
 userapps/bin/newProg
 userapps/bin/newPythonProg
 userapps/bin/nibFrag
 userapps/bin/nibSize
 userapps/bin/nt4Frag
 userapps/bin/paraFetch
 userapps/bin/paraSync
-userapps/bin/pslLiftSubrangeBlat
+userapps/bin/pslMap
+userapps/bin/pslMapPostChain
 userapps/bin/pslPosTarget
+userapps/bin/pslProtToRnaCoords
+userapps/bin/pslRc
 userapps/bin/pslRemoveFrameShifts
 userapps/bin/pslScore
+userapps/bin/pslSpliceJunctions
+userapps/bin/pslSwap
 userapps/bin/pslToPslx
 userapps/bin/pslToXa
-userapps/bin/raSqlQuery
 userapps/bin/raToLines
 userapps/bin/raToTab
 userapps/bin/randomLines
 userapps/bin/rmFaDups
 userapps/bin/rowsToCols
-userapps/bin/scaffoldFaToAgp
 userapps/bin/scrambleFa
 userapps/bin/sizeof
 userapps/bin/spacedToTab
 userapps/bin/splitFile
 userapps/bin/splitFileByColumn
 userapps/bin/strexCalc
 userapps/bin/stringify
 userapps/bin/subChar
 userapps/bin/subColumn
 userapps/bin/subs
+userapps/bin/tabToMmHash
 userapps/bin/tableSum
 userapps/bin/tailLines
+userapps/bin/tdbRename
+userapps/bin/tdbSort
 userapps/bin/textHist2
 userapps/bin/textHistogram
 userapps/bin/tickToDate
 userapps/bin/toLower
 userapps/bin/toUpper
 userapps/bin/trackDbIndexBb
 userapps/bin/twoBitDup
 userapps/bin/twoBitInfo
 userapps/bin/twoBitToFa
+userapps/bin/ucscApiClient
 userapps/bin/udcCleanup
 userapps/bin/undupFa
 userapps/bin/upper
 userapps/bin/vcfFilter
 userapps/bin/venn
 userapps/bin/verticalSplitSqlTable
+userapps/bin/webSync
 userapps/bin/weedLines
 userapps/bin/wigCorrelate
 userapps/bin/wigToBigWig
 userapps/bin/wordLine