diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 26105d1a65ba..7adcd1d6051d 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,60 +1,61 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v DISTVERSION= 1.0.7 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ library and CLI tools for parsing and manipulating VCF files WWW= https://github.com/vcflib/vcflib LICENSE= MIT NOT_FOR_ARCHS= armv6 armv7 NOT_FOR_ARCHS_REASON= requires OpenMP which is not supported BUILD_DEPENDS= pybind11>0:devel/pybind11 LIB_DEPENDS= libhts.so:biology/htslib \ libcurl.so:ftp/curl \ libwfa2.so:biology/wfa2-lib USES= cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix USE_GITHUB= yes GH_ACCOUNT= ekg GH_TUPLE= ekg:fastahack:bb33265:fastahack/contrib/fastahack \ ekg:filevercmp:df20dcc:filevercmp/contrib/filevercmp \ ekg:fsom:56695e1:fsom/contrib/fsom \ ekg:intervaltree:aa59377:intervaltree/contrib/intervaltree \ edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \ ekg:multichoose:e1f94ae:multichoose/contrib/multichoose \ ekg:smithwaterman:2610e25:smithwaterman/contrib/smithwaterman \ simd-everywhere:simde-no-tests:9af03cd:simd/src/simde \ vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp SHEBANG_FILES= scripts/* # FIXME: Add Zig option + lang/zig dep OPTIONS_DEFINE= ZIG OPTIONS_DEFAULT= OPTIONS_SUB= yes ZIG_DESC= Include Zig language support ZIG_BUILD_DEPENDS= zig010>0:lang/zig010 CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so ZIG_CMAKE_OFF= -DZIG=OFF # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 CONFLICTS_INSTALL= filevercmp libdisorder # include/disorder.h include/filevercmp.h include/pdflib.hpp .include post-stage: ${MV} ${STAGEDIR}${PREFIX}/bin/libvcflib.a ${STAGEDIR}${PREFIX}/lib .if ${PORT_OPTIONS:MZIG} ${MV} ${STAGEDIR}/usr/lib/libzig.a ${STAGEDIR}${PREFIX}/lib .endif .include diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt index 263e3dbee0f9..4203916395af 100644 --- a/biology/vcflib/files/patch-CMakeLists.txt +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -1,20 +1,26 @@ ---- CMakeLists.txt.orig 2023-01-29 04:57:02 UTC +--- CMakeLists.txt.orig 2023-02-07 17:22:46 UTC +++ CMakeLists.txt -@@ -9,7 +9,7 @@ +@@ -9,7 +9,7 @@ project(vcflib) cmake_minimum_required(VERSION 3.16) project(vcflib) -set(CMAKE_CXX_STANDARD 17) +set(CMAKE_CXX_STANDARD 14) include(ExternalProject) include(FeatureSummary) -@@ -69,7 +69,7 @@ if(NOT CMAKE_BUILD_TYPE) +@@ -69,7 +69,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) endif() if (${CMAKE_BUILD_TYPE} MATCHES Release) - set(EXTRA_FLAGS "-march=native -D_FILE_OFFSET_BITS=64") + set(EXTRA_FLAGS "-D_FILE_OFFSET_BITS=64") # set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast endif() +@@ -570,4 +570,4 @@ install(FILES ${INCLUDES} DESTINATION include) + + install(FILES ${INCLUDES} DESTINATION include) + +-install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1) ++install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1) diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 297ee6aaa750..b612a8ab875b 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -1,250 +1,250 @@ bin/abba-baba bin/bFst bin/bed2region bin/bgziptabix bin/dumpContigsFromHeader bin/genotypeSummary bin/hapLrt bin/iHS bin/meltEHH bin/normalize-iHS bin/pFst bin/pVst bin/permuteGPAT++ bin/permuteSmooth bin/plotHaps bin/popStats bin/segmentFst bin/segmentIhs bin/sequenceDiversity bin/smoother bin/vcf2bed.py bin/vcf2dag bin/vcf2fasta bin/vcf2sqlite.py bin/vcf2tsv bin/vcf_strip_extra_headers bin/vcfaddinfo bin/vcfafpath bin/vcfallelicprimitives bin/vcfaltcount bin/vcfannotate bin/vcfannotategenotypes bin/vcfbiallelic bin/vcfbreakmulti bin/vcfcat bin/vcfcheck bin/vcfclassify bin/vcfcleancomplex bin/vcfclearid bin/vcfclearinfo bin/vcfcombine bin/vcfcommonsamples bin/vcfcomplex bin/vcfcountalleles bin/vcfcreatemulti bin/vcfdistance bin/vcfecho bin/vcfentropy bin/vcfevenregions bin/vcffilter bin/vcffirstheader bin/vcffixup bin/vcfflatten bin/vcfgeno2alleles bin/vcfgeno2haplo bin/vcfgenosamplenames bin/vcfgenosummarize bin/vcfgenotypecompare bin/vcfgenotypes bin/vcfglbound bin/vcfglxgt bin/vcfgtcompare.sh bin/vcfhetcount bin/vcfhethomratio bin/vcfindelproximity bin/vcfindels bin/vcfindex bin/vcfinfo2qual bin/vcfinfosummarize bin/vcfintersect bin/vcfjoincalls bin/vcfkeepgeno bin/vcfkeepinfo bin/vcfkeepsamples bin/vcfld bin/vcfleftalign bin/vcflength bin/vcfmultiallelic bin/vcfmultiway bin/vcfmultiwayscripts bin/vcfnobiallelicsnps bin/vcfnoindels bin/vcfnosnps bin/vcfnulldotslashdot bin/vcfnullgenofields bin/vcfnumalt bin/vcfoverlay bin/vcfparsealts bin/vcfplotaltdiscrepancy.r bin/vcfplotaltdiscrepancy.sh bin/vcfplotsitediscrepancy.r 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