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# $FreeBSD$
PORTNAME= canu
DISTVERSIONPREFIX= v
DISTVERSION= 1.8
PORTREVISION= 3
CATEGORIES= biology java perl5
MAINTAINER= jwb@FreeBSD.org
COMMENT= Single molecule sequence assembler
LICENSE= GPLv2
LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
LIB_DEPENDS= libboost_regex.so:devel/boost-libs
RUN_DEPENDS= gnuplot:math/gnuplot
USES= compiler:openmp gmake perl5
USE_JAVA= yes
USE_GITHUB= yes
JAVA_RUN= yes
JAVA_VERSION= 1.8+
GH_ACCOUNT= marbl
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
.include <bsd.port.pre.mk>
# GCC 4.2.1 (still base compiler on some 2nd tier platforms) cannot build canu
.if ${COMPILER_TYPE} == gcc && ${COMPILER_VERSION} <= 42
USE_GCC= yes
.endif
pre-configure:
@${REINPLACE_CMD} \
-e 's|-O4||g' \
-e 's|-funroll-loops||g' \
-e 's|-fexpensive-optimizations||g' \
${WRKSRC}/Makefile
@${REINPLACE_CMD} \
-e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
${WRKSRC}/pipelines/canu/OverlapMhap.pm
@${REINPLACE_CMD} \
-e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
${WRKSRC}/pipelines/canu.pl
# Upstream does not want to use lib/perl5/site_perl
post-build:
@${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \
${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
do-install:
@${MKDIR} ${STAGEDIR}${PREFIX}
(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
# STRIP_CMD fails without this on 11.1 under poudriere
@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
@${STRIP_CMD} \
`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
.include <bsd.port.post.mk>
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