git: 372104dd71f6 - main - biology/ugene: fix build on aarch64

The branch main has been updated by fuz:

URL: https://cgit.FreeBSD.org/ports/commit/?id=372104dd71f6e0b1d463713793510b0f7ca5f0a8

commit 372104dd71f6e0b1d463713793510b0f7ca5f0a8
Author:     Robert Clausecker <fuz@FreeBSD.org>
AuthorDate: 2026-04-19 19:39:38 +0000
Commit:     Robert Clausecker <fuz@FreeBSD.org>
CommitDate: 2026-04-21 20:14:30 +0000

    biology/ugene: fix build on aarch64
    
    The bundled copy of htslib is missing required assembly source files,
    causing build failure due to undefined symbols an aarch64.
    Unbundle htslib and use our working port biology/htslib instead.
    
    Approved by:    makc (maintainer)
    MFH:            2026Q2
    PR:             293379
---
 biology/ugene/Makefile                             |  7 ++-
 ...atch-src_libs__3rdparty_samtools_CMakeLists.txt | 70 ++++++++++++++++++++++
 2 files changed, 74 insertions(+), 3 deletions(-)

diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile
index 60d26dd34b52..ab0147da399c 100644
--- a/biology/ugene/Makefile
+++ b/biology/ugene/Makefile
@@ -1,5 +1,6 @@
 PORTNAME=	ugene
 PORTVERSION=	53.1
+PORTREVISION=	1
 CATEGORIES=	biology science
 
 MAINTAINER=	makc@FreeBSD.org
@@ -9,12 +10,12 @@ WWW=		https://ugene.net/
 LICENSE=	GPLv2+
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-IGNORE_aarch64=	fails to build: https://bugs.freebsd.org/293379
-
+LIB_DEPENDS=	libhts.so:biology/htslib
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		cmake compiler:c++14-lang desktop-file-utils gl \
-		localbase:ldflags qt:5 shared-mime-info shebangfix xorg
+		localbase:ldflags pkgconfig qt:5 shared-mime-info \
+		shebangfix xorg
 USE_GL=		gl glu
 USE_QT=		buildtools:build linguisttools:build qmake:build \
 		core gui network networkauth printsupport \
diff --git a/biology/ugene/files/patch-src_libs__3rdparty_samtools_CMakeLists.txt b/biology/ugene/files/patch-src_libs__3rdparty_samtools_CMakeLists.txt
new file mode 100644
index 000000000000..9e066dacc262
--- /dev/null
+++ b/biology/ugene/files/patch-src_libs__3rdparty_samtools_CMakeLists.txt
@@ -0,0 +1,70 @@
+--- src/libs_3rdparty/samtools/CMakeLists.txt.orig	2026-03-01 18:44:47 UTC
++++ src/libs_3rdparty/samtools/CMakeLists.txt
+@@ -21,45 +21,6 @@ file(GLOB SRCS
+ #endif ()
+ 
+ file(GLOB SRCS
+-        src/samtools_core/htslib/cram/cram_codecs.c
+-        src/samtools_core/htslib/cram/cram_decode.c
+-        src/samtools_core/htslib/cram/cram_encode.c
+-        src/samtools_core/htslib/cram/cram_external.c
+-        src/samtools_core/htslib/cram/cram_index.c
+-        src/samtools_core/htslib/cram/cram_io.c
+-        src/samtools_core/htslib/cram/cram_stats.c
+-        src/samtools_core/htslib/cram/mFILE.c
+-        src/samtools_core/htslib/cram/open_trace_file.c
+-        src/samtools_core/htslib/cram/pooled_alloc.c
+-        src/samtools_core/htslib/cram/string_alloc.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/arith_dynamic.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/fqzcomp_qual.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/htscodecs.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/pack.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/rANS_static.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/rANS_static32x16pr.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/rle.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/tokenise_name3.c
+-        src/samtools_core/htslib/htscodecs/htscodecs/utils.c
+-        src/samtools_core/htslib/bgzf.c
+-        src/samtools_core/htslib/errmod.c
+-        src/samtools_core/htslib/header.c
+-        src/samtools_core/htslib/hfile.c
+-        src/samtools_core/htslib/hts.c
+-        src/samtools_core/htslib/hts_expr.c
+-        src/samtools_core/htslib/hts_os.c
+-        src/samtools_core/htslib/kstring.c
+-        src/samtools_core/htslib/md5.c
+-        src/samtools_core/htslib/multipart.c
+-        src/samtools_core/htslib/probaln.c
+-        src/samtools_core/htslib/realn.c
+-        src/samtools_core/htslib/region.c
+-        src/samtools_core/htslib/sam.c
+-        src/samtools_core/htslib/sam_mods.c
+-        src/samtools_core/htslib/tbx.c
+-        src/samtools_core/htslib/textutils.c
+-        src/samtools_core/htslib/thread_pool.c
+         src/samtools_core/bam.c
+         src/samtools_core/bam_aux.c
+         src/samtools_core/bam_lpileup.c
+@@ -233,13 +194,19 @@ endif ()
+     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w")
+ endif ()
+ 
++find_package(PkgConfig REQUIRED)
++pkg_check_modules(HTSLIB REQUIRED htslib)
++
+ add_library(samtools STATIC ${SRCS})
+ 
++target_include_directories(samtools PRIVATE ${HTSLIB_INCLUDE_DIRS})
++target_compile_options(samtools PRIVATE ${HTSLIB_CFLAGS_OTHER})
+ target_link_libraries(samtools
++	${HTSLIB_LIBRARIES}
+         Qt5::Core
+ #        U2Core
+         zlib)
+ 
+ #target_compile_options(samtools PRIVATE
+ #        /we4013         # Treat implicit declarations as errors
+-#)
+\ No newline at end of file
++#)