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# $FreeBSD$
PORTNAME= bowtie
DISTVERSIONPREFIX= v
DISTVERSION= 1.1.2
PORTREVISION= 8
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Ultrafast, memory-efficient short read aligner
LICENSE= ART10
# May also work on other 64-bit platforms, but untested
ONLY_FOR_ARCHS= amd64
# FIXME: bowtie-align intermittently dumps core when compiled with clang
# GCC 4.2 does not provide good performance
USES= gmake perl5 python:run shebangfix
USE_GCC= yes
USE_PERL5= run
USE_GITHUB= yes
SHEBANG_FILES= scripts/*.pl bowtie bowtie-build bowtie-inspect
GH_ACCOUNT= BenLangmead
OPTIONS_DEFINE= DOCS
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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