PORTNAME=	cufflinks
DISTVERSIONPREFIX=	v
DISTVERSION=	2.2.1-89
PORTREVISION=	13
DISTVERSIONSUFFIX=	-gdc3b0cb
CATEGORIES=	biology

PATCH_SITES=	https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/
PATCHFILES+=	ea4671149f3054c773d99cea521db75bf7b0658f.patch:-p1 # https://github.com/cole-trapnell-lab/cufflinks/pull/127

MAINTAINER=	yuri@FreeBSD.org
COMMENT=	Cufflinks assembles transcripts, estimates their abundance, etc
WWW=		https://cole-trapnell-lab.github.io/cufflinks/

LICENSE=	BSL
LICENSE_FILE=	${WRKSRC}/LICENSE

LIB_DEPENDS=	libboost_thread.so:devel/boost-libs \
		libhts.so:biology/htslib

USES=		autoreconf compiler:c++11-lang eigen:3 gmake python shebangfix

SHEBANG_FILES=	src/cuffmerge

GNU_CONFIGURE=	yes

USE_GITHUB=	yes
GH_ACCOUNT=	cole-trapnell-lab

CXXFLAGS+=	-I${LOCALBASE}/include/eigen3
CFLAGS+=	-I${LOCALBASE}/include/eigen3 # https://github.com/cole-trapnell-lab/cufflinks/issues/113

CONFLICTS_INSTALL=	gffread

PLIST_FILES=	bin/compress_gtf \
		bin/cuffcompare \
		bin/cuffdiff \
		bin/cufflinks \
		bin/cuffmerge \
		bin/cuffnorm \
		bin/cuffquant \
		bin/gffread \
		bin/gtf_to_sam

post-patch: # https://github.com/cole-trapnell-lab/cufflinks/issues/116
	@${GREP} -rl 'fabs(' ${WRKSRC} | ${GREP} "\.cpp$$" | ${XARGS} ${REINPLACE_CMD} 's|std::fabs(|fabs(| ; s|fabs(|::fabs(|'
	@${REINPLACE_CMD} -e '/boost_system/d'  -e '/AX_BOOST_SYSTEM/d' \
		${WRKSRC}/configure.ac

.include <bsd.port.mk>
