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PORTNAME= bwa
PORTVERSION= 0.7.17
DISTVERSIONPREFIX=v
CATEGORIES= biology
PATCH_SITES= https://github.com/lh3/bwa/commit/
PATCHFILES= 2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch:-p1
MAINTAINER= jwb@FreeBSD.org
COMMENT= Burrows-Wheeler sequence aligner
LICENSE= GPLv3
# From 0.7.9a: Recheck for 0.7.17.
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_mips= fails to compile: cc1: unrecognized command line option "-msse2"
BROKEN_mips64= fails to compile: cc1: unrecognized command line option "-msse2"
BROKEN_powerpc64= fails to compile: ksw.c: emmintrin.h: No such file or directory
BROKEN_riscv64= fails to compile: invalid conversion between vector type and integer type
USES= gmake perl5 shebangfix tar:bzip2
SHEBANG_FILES= qualfa2fq.pl xa2multi.pl
USE_PERL5= run
USE_GITHUB= yes
GH_ACCOUNT= lh3
PLIST_FILES= bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl man/man1/bwa.1.gz
.include <bsd.port.options.mk>
.if ${ARCH} == amd64 || ${ARCH} == i386
# Avoid #error in emmintrin.h
CFLAGS+= -msse2
.elif ${ARCH} == powerpc64le
CFLAGS+= -DNO_WARN_X86_INTRINSICS
USES+= compiler:gcc-c++11-lib
.endif
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${STAGEDIR}${PREFIX}/bin
${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MAN1PREFIX}/man/man1
.include <bsd.port.mk>
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