# $NetBSD$
#
###########################################################
#                  Generated by fbsd2pkg                  #
#              Thu Mar  3 09:54:03 CST 2016               #
###########################################################

DISTNAME=	tophat-${PORTVERSION}
CATEGORIES=	biology
# Note: Distfiles on Github are not the same as those here
MASTER_SITES=	http://ccb.jhu.edu/software/tophat/downloads/

MAINTAINER=	bacon@NetBSD.org
HOMEPAGE=	https://ccb.jhu.edu/software/tophat/index.shtml
COMMENT=	Fast splice junction mapper for RNA-Seq reads
LICENSE=	boost-license

MAKE_JOBS_SAFE=	no

DEPENDS+=	bowtie2>=0:../../wip/bowtie2

USE_LANGUAGES=	c c++
USE_TOOLS+=	gmake
GNU_CONFIGURE=	yes

REPLACE_PYTHON=	src/bed_to_juncs
REPLACE_PYTHON=	src/contig_to_chr_coords
REPLACE_PYTHON=	src/sra_to_solid
REPLACE_PYTHON=	src/tophat-fusion-post
REPLACE_PYTHON=	src/tophat.py
REPLACE_BASH=	src/tophat2.sh

CFLAGS+=	-Wno-unused

PORTVERSION=	2.1.1

.include "../../devel/zlib/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../devel/boost-libs/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
