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49 lines
1.3 KiB
Makefile
49 lines
1.3 KiB
Makefile
PORTNAME= cufflinks
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DISTVERSIONPREFIX= v
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DISTVERSION= 2.2.1-89
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PORTREVISION= 9
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DISTVERSIONSUFFIX= -gdc3b0cb
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CATEGORIES= biology
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PATCH_SITES= https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/
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PATCHFILES+= ea4671149f3054c773d99cea521db75bf7b0658f.patch:-p1 # https://github.com/cole-trapnell-lab/cufflinks/pull/127
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Cufflinks assembles transcripts, estimates their abundance, etc
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WWW= https://cole-trapnell-lab.github.io/cufflinks/
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LICENSE= BSL
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LICENSE_FILE= ${WRKSRC}/LICENSE
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LIB_DEPENDS= libboost_system.so:devel/boost-libs \
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libhts.so:biology/htslib
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USES= autoreconf compiler:c++11-lang eigen:3 gmake python shebangfix
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SHEBANG_FILES= src/cuffmerge
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GNU_CONFIGURE= yes
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USE_GITHUB= yes
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GH_ACCOUNT= cole-trapnell-lab
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CXXFLAGS+= -I${LOCALBASE}/include/eigen3
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CFLAGS+= -I${LOCALBASE}/include/eigen3 # https://github.com/cole-trapnell-lab/cufflinks/issues/113
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CONFLICTS_INSTALL= gffread
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PLIST_FILES= bin/compress_gtf \
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bin/cuffcompare \
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bin/cuffdiff \
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bin/cufflinks \
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bin/cuffmerge \
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bin/cuffnorm \
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bin/cuffquant \
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bin/gffread \
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bin/gtf_to_sam
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post-patch: # https://github.com/cole-trapnell-lab/cufflinks/issues/116
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@${GREP} -rl 'fabs(' ${WRKSRC} | ${GREP} "\.cpp$$" | ${XARGS} ${REINPLACE_CMD} 's|std::fabs(|fabs(| ; s|fabs(|::fabs(|'
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.include <bsd.port.mk>
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