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	COMMENT= Cufflinks assembles transcripts, estimates their abundance, etc			COMMENT= Cufflinks assembles transcripts, estimates their abundance, etc

	LICENSE= BSL			LICENSE= BSL
	LICENSE_FILE= ${WRKSRC}/LICENSE			LICENSE_FILE= ${WRKSRC}/LICENSE

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

	BROKEN= error: expected ';' at end of declaration

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

	SHEBANG_FILES= src/cuffmerge			SHEBANG_FILES= src/cuffmerge

	GNU_CONFIGURE= yes			GNU_CONFIGURE= yes

	USE_GITHUB= yes			USE_GITHUB= yes
	GH_ACCOUNT= cole-trapnell-lab			GH_ACCOUNT= cole-trapnell-lab

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

	CONFLICTS_INSTALL= gffread			CONFLICTS_INSTALL= gffread

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