76 lines
2.9 KiB
Makefile
76 lines
2.9 KiB
Makefile
# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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###########################################################
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# Do not upgrade to 2.2.1 until crash bugs are worked out
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DISTNAME= cufflinks-${PORTVERSION}
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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= dsiercks@uwm.edu
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HOMEPAGE= http://port.home.page/
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COMMENT= Transcript assembly, differential expression, regulation for RNA-Seq
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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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REPLACE_PYTHON= src/cuffmerge
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# FIXME: boost problem with long double and hackaround: https://svn.boost.org/trac/boost/query?status=!closed&page=3&order=summary&row=description: #9331
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# Just using double instead for now
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SUBST_CLASSES+= boost
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SUBST_STAGE.boost= post-patch
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SUBST_SED.boost+= -e 's|shared_ptr|boost::shared_ptr|g'
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SUBST_SED.boost+= -e 's|boost::shared_ptr.hpp|shared_ptr.hpp|g'
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SUBST_SED.boost+= -e 's|boost::boost::|boost::|g'
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SUBST_SED.boost+= -e 's|^mutex|boost::mutex|g'
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SUBST_SED.boost+= -e 's|logl|log|g'
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SUBST_SED.boost+= -e 's|long double|double|g'
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SUBST_SED.boost+= -e 's|Lf|lf|g'
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SUBST_SED.boost+= -e 's|Lg|lg|g'
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SUBST_FILES.boost+= ${WRKSRC}/src/abundances.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/abundances.h
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SUBST_FILES.boost+= ${WRKSRC}/src/assemble.h
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SUBST_FILES.boost+= ${WRKSRC}/src/biascorrection.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/biascorrection.h
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SUBST_FILES.boost+= ${WRKSRC}/src/bundles.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/bundles.cpp.orig
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SUBST_FILES.boost+= ${WRKSRC}/src/bundles.h
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SUBST_FILES.boost+= ${WRKSRC}/src/clustering.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/common.h
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SUBST_FILES.boost+= ${WRKSRC}/src/compress_gtf.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/cuffdiff.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/cufflinks.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/differential.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/differential.h
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SUBST_FILES.boost+= ${WRKSRC}/src/filters.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/filters.h
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SUBST_FILES.boost+= ${WRKSRC}/src/gtf_to_sam.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/hits.h
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SUBST_FILES.boost+= ${WRKSRC}/src/replicates.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/replicates.h
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SUBST_FILES.boost+= ${WRKSRC}/src/scaffolds.cpp
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SUBST_FILES.boost+= ${WRKSRC}/src/scaffolds.h
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SUBST_CLASSES+= boolint
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SUBST_STAGE.boolint= post-patch
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SUBST_FILES.boolint= ${WRKSRC}/src/rounding.h
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SUBST_SED.boolint+= -e 's|int& is_up|bool\& is_up|g'
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CONFIGURE_ARGS+= --with-bam=${PREFIX}/samtools0119 --with-boost
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CFLAGS+= -I${PREFIX}/include/eigen3
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LDFLAGS+= -lboost_system -lboost_iostreams -lboost_thread
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PORTVERSION= 2.1.1
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.include "../../lang/python/application.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../math/eigen3/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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.include "../../wip/samtools0119/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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