54 lines
2.1 KiB
Makefile
54 lines
2.1 KiB
Makefile
PORTNAME= freebayes
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.2.0
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PORTREVISION= 3
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping
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LICENSE= MIT
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BROKEN_aarch64= fails to compile: invalid conversion between vector type and integer type
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BROKEN_armv6= fails to compile: invalid conversion between vector type and integer type
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BROKEN_armv7= fails to compile: invalid conversion between vector type and integer type
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BROKEN_riscv64= fails to compile: invalid conversion between vector type and integer type
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# Submodules use older versions than the ports, so we cannot safely unbundle
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# No shared libs are built by the submodules so there will be no conflicts
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USES= compiler:c++11-lang gmake tar:xz
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USE_GITHUB= yes
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GH_ACCOUNT= ekg
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GH_TUPLE= walaj:SeqLib:5941c68:SeqLib/SeqLib-temp \
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jwalabroad:bwa:c02766e:bwa/SeqLib/bwa \
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jwalabroad:fermi-lite:5bc90f8:fermi/SeqLib/fermi-lite \
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samtools:htslib:49fdfbd:htslib/SeqLib/htslib \
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ekg:bamtools:e77a43f:bamtools/bamtools \
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ekg:intervaltree:dbb4c51:interval1/intervaltree \
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vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \
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ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \
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ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \
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ekg:fsom:a6ef318:fsom/vcflib/fsom \
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google:googletest:d225acc:google/vcflib/googletest \
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ekg:intervaltree:b704f19:interval2/vcflib/intervaltree \
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ekg:multichoose:73d35da:multichoose/vcflib/multichoose \
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ekg:smithwaterman:84c08d7:smithwaterman/vcflib/smithwaterman \
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ekg:tabixpp:80012f8:tabixpp/vcflib/tabixpp \
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samtools:htslib:0f298ce:hts2/vcflib/tabixpp/htslib
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# GCC disables sse2 by default on i386, but it's required for vcflib
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CXXFLAGS+= --std=c++11
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CFLAGS_i386= -msse2
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MAKE_JOBS_UNSAFE= yes
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PLIST_FILES= bin/bamleftalign bin/freebayes
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# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around
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# by dumping the parent in a temp directory and then moving the contents
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post-extract:
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${MV} -n ${WRKSRC}/SeqLib-temp/* ${WRKSRC}/SeqLib
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${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib
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do-install:
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${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.mk>
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