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PORTNAME= augustus
DISTVERSIONPREFIX= v
DISTVERSION= 3.5.0
PORTREVISION= 9
CATEGORIES= biology science
PKGNAMESUFFIX= -gene-prediction
MAINTAINER= yuri@FreeBSD.org
COMMENT= Genome annotation tool
WWW= http://bioinf.uni-greifswald.de/webaugustus/
LICENSE= GPLv3
LIB_DEPENDS= libbamtools.so:biology/bamtools \
libboost_iostreams.so:devel/boost-libs \
libcolamd.so:math/suitesparse-colamd \
libgsl.so:math/gsl \
libhts.so:biology/htslib \
liblpsolve55.so:math/lp_solve \
libmysqlpp.so:databases/mysql++
RUN_DEPENDS= samtools:biology/samtools
USES= gmake localbase:ldflags mysql perl5 python sqlite shebangfix
USE_CXXSTD= c++14
USE_GITHUB= yes
GH_ACCOUNT= Gaius-Augustus
GH_PROJECT= Augustus
SHEBANG_GLOB= *.pl *.py
SHEBANG_FILES= scripts/checkUTR
CXXFLAGS+= -I${LOCALBASE}/include/bamtools \
-I${LOCALBASE}/include/lpsolve \
-I${LOCALBASE}/include/mysql
LDFLAGS+= -L${LOCALBASE}/lib/mysql
MAKE_ARGS= INSTALLDIR=${LOCALBASE}/${PORTNAME} RLN="${RLN}"
BINARY_ALIAS= make=${GMAKE} python3=${PYTHON_CMD}
TEST_TARGET= test
post-install:
@${STRIP_CMD} ${STAGEDIR}${PREFIX}/${PORTNAME}/bin/*
@${RM} ${STAGEDIR}${PREFIX}/${PORTNAME}/scripts/pasapolyA2hints.pl.orig
.include <bsd.port.mk>
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