# Created by: Jason Bacon <bacon4000@gmail.com>
# $FreeBSD: head/biology/bowtie/Makefile 410180 2016-03-05 13:21:26Z rakuco $

PORTNAME=		bowtie
PORTVERSION=		1.1.2
DISTVERSIONPREFIX=	v
CATEGORIES=		biology

MAINTAINER=	bacon4000@gmail.com
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
USE_GCC=	yes
USES=		gmake perl5 shebangfix
USE_PERL5=	run
SHEBANG_FILES=	scripts/*.pl

USE_GITHUB=	yes
GH_ACCOUNT=	BenLangmead

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>