diff options
Diffstat (limited to 'biology/freebayes/Makefile')
| -rw-r--r-- | biology/freebayes/Makefile | 53 |
1 files changed, 24 insertions, 29 deletions
diff --git a/biology/freebayes/Makefile b/biology/freebayes/Makefile index 225643cec02b..9ca877a4c665 100644 --- a/biology/freebayes/Makefile +++ b/biology/freebayes/Makefile @@ -1,7 +1,6 @@ PORTNAME= freebayes DISTVERSIONPREFIX= v -DISTVERSION= 1.2.0 -PORTREVISION= 3 +DISTVERSION= 1.3.5 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -9,46 +8,42 @@ COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping LICENSE= MIT -BROKEN_aarch64= fails to compile: invalid conversion between vector type and integer type +# These should be rechecked: Same error resolved on aarch64 in 1.3.5 update. BROKEN_armv6= fails to compile: invalid conversion between vector type and integer type BROKEN_armv7= fails to compile: invalid conversion between vector type and integer type BROKEN_riscv64= fails to compile: invalid conversion between vector type and integer type +LIB_DEPENDS= libhts.so:biology/htslib \ + libtabix.so:biology/tabixpp + # Submodules use older versions than the ports, so we cannot safely unbundle # No shared libs are built by the submodules so there will be no conflicts -USES= compiler:c++11-lang gmake tar:xz +USES= compiler:c++14-lang localbase meson perl5 pkgconfig USE_GITHUB= yes GH_ACCOUNT= ekg -GH_TUPLE= walaj:SeqLib:5941c68:SeqLib/SeqLib-temp \ - jwalabroad:bwa:c02766e:bwa/SeqLib/bwa \ - jwalabroad:fermi-lite:5bc90f8:fermi/SeqLib/fermi-lite \ - samtools:htslib:49fdfbd:htslib/SeqLib/htslib \ - ekg:bamtools:e77a43f:bamtools/bamtools \ - ekg:intervaltree:dbb4c51:interval1/intervaltree \ - vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \ - ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \ - ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \ +GH_TUPLE= ekg:vcflib:d4073c3:vcflib/vcflib-temp \ + ekg:smithwaterman:2610e25:smithwaterman/vcflib/smithwaterman \ + ekg:multichoose:68733cd:multichoose/vcflib/multichoose \ + ekg:fastahack:bb33265:fastahack/vcflib/fastahack \ + ekg:intervaltree:17ddd57:intervaltree/vcflib/intervaltree \ ekg:fsom:a6ef318:fsom/vcflib/fsom \ - google:googletest:d225acc:google/vcflib/googletest \ - ekg:intervaltree:b704f19:interval2/vcflib/intervaltree \ - ekg:multichoose:73d35da:multichoose/vcflib/multichoose \ - ekg:smithwaterman:84c08d7:smithwaterman/vcflib/smithwaterman \ - ekg:tabixpp:80012f8:tabixpp/vcflib/tabixpp \ - samtools:htslib:0f298ce:hts2/vcflib/tabixpp/htslib - -# GCC disables sse2 by default on i386, but it's required for vcflib -CXXFLAGS+= --std=c++11 -CFLAGS_i386= -msse2 -MAKE_JOBS_UNSAFE= yes + ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \ + google:googletest:d225acc:googletest/vcflib/googletest \ + edawson:libVCFH:615a06b:libVCFH/vcflib/libVCFH \ + simd-everywhere:simde-no-tests:2931676:simd/vcflib/src/simde \ + ekg:intervaltree:b90527f:intervaltree2/intervaltree \ + ekg:tabixpp:b255df1:tabixpp/vcflib/tabixpp \ + ingydotnet:test-simple-bash:124673f:testsimplebash/test/test-simple-bash \ + illusori:bash-tap:c38fbfa:bashtap/test/bash-tap \ + samtools:htslib:b581944:htslib/contrib/htslib +USE_PERL5= build + +LDFLAGS+= -lexecinfo PLIST_FILES= bin/bamleftalign bin/freebayes # GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around # by dumping the parent in a temp directory and then moving the contents post-extract: - ${MV} -n ${WRKSRC}/SeqLib-temp/* ${WRKSRC}/SeqLib - ${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib - -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin + ${CP} -r ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib .include <bsd.port.mk> |