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PORTNAME= freebayes
DISTVERSIONPREFIX= v
DISTVERSION= 1.2.0
PORTREVISION= 3
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping
LICENSE= MIT
BROKEN_aarch64= fails to compile: invalid conversion between vector type and integer type
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
# 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
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 \
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
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
.include <bsd.port.mk>
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