diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 60d26dd34b52..ab0147da399c 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -1,80 +1,81 @@ PORTNAME= ugene PORTVERSION= 53.1 +PORTREVISION= 1 CATEGORIES= biology science MAINTAINER= makc@FreeBSD.org COMMENT= Integrated bioinformatics toolkit 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 \ svg testlib websockets widgets xml \ imageformats:run USE_XORG= x11 xtst USE_LDCONFIG= ${UGENE_LIBDIR} USE_GITHUB= yes GH_ACCOUNT= ugeneunipro CXXFLAGS_i386= -msse2 LDFLAGS+= -pthread SHEBANG_FILES= etc/shared/ugene PORTDATA= * UGENE_LIBDIR= ${PREFIX}/lib/ugene .include .if empty(ARCH:Mamd64) && empty(ARCH:Mi386) BUILD_DEPENDS+= ${LOCALBASE}/include/sse2neon.h:devel/sse2neon .endif post-patch: @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp ${REINPLACE_CMD} 's,stdc++fs,,' \ ${WRKSRC}/src/libs_3rdparty/QSpec/CMakeLists.txt ${REINPLACE_CMD} 's,/usr/local/share/ugene,${DATADIR},' \ ${WRKSRC}/src/ugenecl/src/Main.cpp # breakpad is not aware of FreeBSD ${REINPLACE_CMD} '/libs_3rdparty\/breakpad/d' \ ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt \ ${WRKSRC}/CMakeLists.txt ${REINPLACE_CMD} 's,breakpad,,' \ ${WRKSRC}/src/ugeneui/CMakeLists.txt \ ${WRKSRC}/src/ugenecl/CMakeLists.txt \ ${WRKSRC}/src/corelibs/U2Private/CMakeLists.txt # Do not alter binary names for debug build ${REINPLACE_CMD} '/DEBUG_POSTFIX/d' \ ${WRKSRC}/src/plugins_checker/CMakeLists.txt \ ${WRKSRC}/src/ugenecl/CMakeLists.txt \ ${WRKSRC}/src/ugenem/CMakeLists.txt \ ${WRKSRC}/src/ugeneui/CMakeLists.txt \ ${WRKSRC}/CMakeLists.txt do-install: ${MKDIR} ${STAGEDIR}/${UGENE_LIBDIR} cd ${BUILD_WRKSRC}/dist && ${COPYTREE_SHARE} . ${STAGEDIR}/${UGENE_LIBDIR}/ .for prog in ugene ugenecl ugenem ugeneui ${RLN} ${STAGEDIR}${UGENE_LIBDIR}/${prog} ${STAGEDIR}/${PREFIX}/bin/${prog} .endfor ${MKDIR} ${STAGEDIR}/${DATADIR} cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}/${DATADIR} ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.desktop ${STAGEDIR}/${DESKTOPDIR} ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.png ${STAGEDIR}/${PREFIX}/share/pixmaps/ ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene-ext.png ${STAGEDIR}/${PREFIX}/share/pixmaps/ ${INSTALL_DATA} ${WRKSRC}/etc/shared/ugene.1.gz ${STAGEDIR}/${PREFIX}/share/man/man1/ ${MKDIR} ${STAGEDIR}/${PREFIX}/share/mime/packages ${INSTALL_DATA} ${WRKSRC}/etc/shared/application-x-ugene.xml ${STAGEDIR}/${PREFIX}/share/mime/packages/ .include 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 ++#)