# $NetBSD$

###########################################################
#               Generated by fbsd2pkg                     #
###########################################################

###################################
# Unconverted FreeBSD port syntax:

# # FIXME: Find logl somewhere instead of falling back to log
# # FIXME: boost problem and hackaround: https://svn.boost.org/trac/boost/query?status=!closed&page=3&order=summary&row=description: #9331
# post-patch:
# 	${REINPLACE_CMD} \
# 		-e 's|logl|log|g' \
# 		-e 's|long double|double|g' \
# 		${WRKSRC}/src/*.cpp \
# 		${WRKSRC}/src/*.h
# .include <bsd.port.mk>

DISTNAME=	cufflinks-2.2.1
CATEGORIES=	biology
MASTER_SITES=	http://cufflinks.cbcb.umd.edu/downloads/

MAINTAINER=	jwbacon@tds.net

COMMENT=	RNA transcript assembly, differential expression/regulation
# LICENSE=	

# Pessimistic assumption.  Test and change if possible.
MAKE_JOBS_SAFE=	no

# Just assuming C and C++: Adjust this!
USE_LANGUAGES=	c c++
GNU_CONFIGURE=	yes

# Darwin

CFLAGS+=	-I${LOCALBASE}/include/eigen3
# These are getting left out on CentOS and Darwin in spite of buildlink
LDFLAGS+=	-L${PREFIX}/lib -lboost_thread -lboost_system -lboost_serialization

# Darwin i386 Snow Leopard doesn't support /bin/arch or /usr/bin/arch -k
SUBST_CLASSES+=		arch
SUBST_STAGE.arch=	post-patch
SUBST_FILES.arch=	configure
SUBST_SED.arch=		's|arch -k|arch|g'

# Allow compiling on i386
SUBST_CLASSES+=		cflags
SUBST_STAGE.cflags=	post-patch
SUBST_FILES.cflags=	configure
SUBST_SED.cflags=	's|-arch x86_64||g'

.include "../../wip/samtools/buildlink3.mk"
.include "../../devel/boost-libs/buildlink3.mk"
.include "../../devel/boost-headers/buildlink3.mk"
.include "../../devel/boost-jam/buildlink3.mk"
# CentOS can't find libbam without this.  samtools buildlink issue?
.include "../../devel/zlib/buildlink3.mk"
.include "../../math/eigen3/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../mk/bsd.pkg.mk"
