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PORTNAME= bowtie
DISTVERSIONPREFIX= v
DISTVERSION= 1.3.1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Ultrafast, memory-efficient short read aligner
WWW= http://bowtie-bio.sourceforge.net/index.shtml
LICENSE= ART10
ONLY_FOR_ARCHS= aarch64 amd64 powerpc64 powerpc64le riscv64
# c++11-lib is just for GCC 4.2-based systems
# Remove it when support officially ends
USES= compiler:c++11-lib gmake perl5 python:run shebangfix
USE_PERL5= run
USE_GITHUB= yes
SHEBANG_FILES= scripts/*.pl bowtie bowtie-build scripts/bowtie-hbb.sh \
bowtie-inspect
GH_ACCOUNT= BenLangmead
OPTIONS_DEFINE= DOCS
.include <bsd.port.options.mk>
.if ${ARCH:Mpowerpc64*} || ${ARCH} == aarch64 || ${ARCH:Mriscv64*}
MAKE_ENV= POPCNT_CAPABILITY=0
.endif
post-install:
${MKDIR} ${STAGEDIR}${DATADIR}/scripts
${INSTALL_SCRIPT} \
${WRKSRC}/bowtie \
${WRKSRC}/bowtie-build \
${WRKSRC}/bowtie-inspect \
${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} \
${WRKSRC}/scripts/*.sh \
${WRKSRC}/scripts/*.pl \
${STAGEDIR}${DATADIR}/scripts
cd ${WRKSRC} && ${COPYTREE_SHARE} \
'genomes indexes reads' \
${STAGEDIR}${DATADIR}
cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \
\* \
${STAGEDIR}${DOCSDIR}
${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*-[sl]
.include <bsd.port.mk>
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