PORTNAME= canu
DISTVERSION= 2.2
PORTREVISION= 7
CATEGORIES= biology java perl5
# Github auto-generated tarballs lack submodules
MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/
MAINTAINER= [email protected]
COMMENT= Single molecule sequence assembler
WWW= https://canu.readthedocs.io/
LICENSE= GPLv2
LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc powerpcspe
NOT_FOR_ARCHS_REASON= Requires 64-bit processor
LIB_DEPENDS= libboost_regex.so:devel/boost-libs
RUN_DEPENDS= gnuplot:math/gnuplot
USES= compiler:c++11-lang gmake java localbase perl5 tar:xz
USE_CXXSTD= c++14
# Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
# using a separate install target.
MAKE_ENV= DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports
WRKSRC_SUBDIR= src
.include <bsd.port.pre.mk>
# Parasail should be unbundled, but that would be a project because it's
# currently woven into the canu code
post-extract:
.if ${ARCH} == "aarch64"
${CP} ${FILESDIR}/cpuid_arm.c ${WRKSRC}/utility/src/parasail/cpuid.c
.elif ${ARCH} == "powerpc64" || ${ARCH} == "powerpc64le"
${CP} ${FILESDIR}/cpuid_ppc.c ${WRKSRC}/utility/src/parasail/cpuid.c
.elif ${ARCH} != "amd64"
${CP} ${FILESDIR}/cpuid_any.c ${WRKSRC}/utility/src/parasail/cpuid.c
.endif
pre-configure:
@${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.post.mk>
