55 lines
1.9 KiB
Makefile
55 lines
1.9 KiB
Makefile
# $NetBSD: Makefile,v 1.1 2014/09/04 21:51:02 outpaddling Exp $
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###########################################################
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# Generated by fbsd2pkg #
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###########################################################
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# This version is known for frequent crashes
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# FIXME: boost problem and hackaround:
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# https://svn.boost.org/trac/boost/query?status=!closed&page=3&order=summary&row=description: #9331
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DISTNAME= cufflinks-2.2.1
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CATEGORIES= biology
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MASTER_SITES= http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/
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MAINTAINER= bacon@NetBSD.org
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COMMENT= RNA transcript assembly, differential expression/regulation
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LICENSE= boost-license
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USE_LANGUAGES= c c++
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GNU_CONFIGURE= yes
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CONFIGURE_ARGS+= --with-bam=${PREFIX}/samtools0119
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# Darwin
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CFLAGS+= -I${PREFIX}/include/eigen3
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# These are getting left out on CentOS and Darwin in spite of buildlink
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LDFLAGS+= -L${PREFIX}/lib -lboost_thread -lboost_system -lboost_serialization
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# Darwin i386 Snow Leopard doesn't support /bin/arch or /usr/bin/arch -k
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SUBST_CLASSES+= arch
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SUBST_STAGE.arch= post-patch
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SUBST_FILES.arch= configure
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SUBST_SED.arch= -e 's|arch -k|arch|g'
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# Allow compiling on i386
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SUBST_CLASSES+= cflags
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SUBST_STAGE.cflags= post-patch
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SUBST_FILES.cflags= configure
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SUBST_SED.cflags= -e 's|-arch x86_64||g'
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SUBST_CLASSES+= ldouble
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SUBST_STAGE.ldouble= post-patch
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SUBST_FILES.ldouble= ${WRKSRC}/src/*.cpp ${WRKSRC}/src/*.h
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SUBST_SED.ldouble= -e 's|logl|log|g'
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SUBST_SED.ldouble+= -e 's|long double|double|g'
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.include "../../wip/samtools0119/buildlink3.mk"
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.include "../../devel/boost-libs/buildlink3.mk"
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.include "../../devel/boost-headers/buildlink3.mk"
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.include "../../devel/boost-jam/buildlink3.mk"
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# CentOS can't find libbam without this. samtools buildlink issue?
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../math/eigen3/buildlink3.mk"
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.include "../../lang/python/application.mk"
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.include "../../mk/bsd.pkg.mk"
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