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PORTNAME= cufflinks
DISTVERSIONPREFIX= v
DISTVERSION= 2.2.1-89
PORTREVISION= 2
DISTVERSIONSUFFIX= -gdc3b0cb
CATEGORIES= biology
PATCH_SITES= https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/
PATCHFILES+= ea4671149f3054c773d99cea521db75bf7b0658f.patch:-p1 # https://github.com/cole-trapnell-lab/cufflinks/pull/127
MAINTAINER= yuri@FreeBSD.org
COMMENT= Cufflinks assembles transcripts, estimates their abundance, etc
LICENSE= BSL
LICENSE_FILE= ${WRKSRC}/LICENSE
LIB_DEPENDS= libboost_system.so:devel/boost-libs \
libhts.so:biology/htslib
USES= autoreconf compiler:c++11-lang eigen:3 gmake python shebangfix
SHEBANG_FILES= src/cuffmerge
GNU_CONFIGURE= yes
USE_GITHUB= yes
GH_ACCOUNT= cole-trapnell-lab
CXXFLAGS+= -I${LOCALBASE}/include/eigen3
CFLAGS+= -I${LOCALBASE}/include/eigen3 # https://github.com/cole-trapnell-lab/cufflinks/issues/113
PLIST_FILES= bin/compress_gtf \
bin/cuffcompare \
bin/cuffdiff \
bin/cufflinks \
bin/cuffmerge \
bin/cuffnorm \
bin/cuffquant \
bin/gffread \
bin/gtf_to_sam
post-patch: # https://github.com/cole-trapnell-lab/cufflinks/issues/116
@${GREP} -rl 'fabs(' ${WRKSRC} | ${GREP} "\.cpp$$" | ${XARGS} ${REINPLACE_CMD} 's|std::fabs(|fabs(| ; s|fabs(|::fabs(|'
.include <bsd.port.mk>
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