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PORTNAME= canu
DISTVERSION= 2.1
PORTREVISION= 1
CATEGORIES= biology java perl5
# Github auto-generated tarballs lack submodules
MASTER_SITES= https://github.com/marbl/canu/releases/download/v2.1/
MAINTAINER= jwb@FreeBSD.org
COMMENT= Single molecule sequence assembler
LICENSE= GPLv2
LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
BROKEN_powerpc64= fails to build: utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field
NOT_FOR_ARCHS= armv6 armv7 i386 powerpc
NOT_FOR_ARCHS_REASON= __int128 is not supported on this target
LIB_DEPENDS= libboost_regex.so:devel/boost-libs
RUN_DEPENDS= gnuplot:math/gnuplot
USES= compiler:c++11-lang gmake localbase perl5
USE_JAVA= yes
JAVA_RUN= yes
JAVA_VERSION= 1.8+
WRKSRC_SUBDIR= src
# Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
# using a separate install target.
MAKE_ENV= DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports
pre-configure:
@${REINPLACE_CMD} \
-e 's|-O4||g' \
-e 's|-funroll-loops||g' \
-e 's|-fexpensive-optimizations||g' \
${WRKSRC}/Makefile
@${REINPLACE_CMD} \
-e 's|RealBin/../lib/site_perl|RealBin/../${SITE_PERL_REL}/canu|g' \
${WRKSRC}/pipelines/canu.pl
# Upstream does not want to use lib/perl5/site_perl
post-build:
@${MKDIR} ${WRKSRC}/build/lib/perl5
${MV} ${WRKSRC}/build/lib/site_perl ${WRKSRC}/build/lib/perl5
do-install:
@${MKDIR} ${STAGEDIR}${PREFIX}
(cd ${WRKSRC}/build && ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
# STRIP_CMD fails without this under poudriere
@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
@${STRIP_CMD} \
`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
(cd ${WRKSRC}/build && \
${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
.include <bsd.port.mk>
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