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# $FreeBSD$
PORTNAME= canu
DISTVERSIONPREFIX= v
DISTVERSION= 1.6
PORTREVISION= 1
CATEGORIES= biology java perl5
MAINTAINER= jwb@FreeBSD.org
COMMENT= Single molecule sequence assembler
LICENSE= GPLv2
LICENSE_FILE= ${WRKSRC}/README.license.GPL
LIB_DEPENDS= libboost_regex.so:devel/boost-libs
RUN_DEPENDS= gnuplot:math/gnuplot
USES= compiler:openmp gmake perl5
USE_JAVA= yes
JAVA_RUN= yes
JAVA_VERSION= 1.8+
USE_GITHUB= yes
GH_ACCOUNT= marbl
BUILD_WRKSRC= ${WRKSRC}/src
# Makefile compiles directly into ${DESTDIR}${PREFIX}
MAKE_ENV+= DESTDIR=${BUILD_WRKSRC}
post-patch:
${REINPLACE_CMD} \
-e 's|-O4||g' \
-e 's|-funroll-loops||g' \
-e 's|-fexpensive-optimizations||g' \
-e 's|amd64|${ARCH}|g' \
${BUILD_WRKSRC}/Makefile
${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
${BUILD_WRKSRC}/pipelines/canu/OverlapMhap.pm
${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
${BUILD_WRKSRC}/pipelines/canu.pl
# Reorganize according to filesystem hierarchy standard
post-build:
@${MKDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${SITE_PERL_REL}
@${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/lib/canu \
${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${SITE_PERL_REL}
@${RMDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/lib
@${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/*.a \
${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib
@${MKDIR} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${JAVAJARDIR:S,^${PREFIX}/,,}
@${MV} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/*.jar \
${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/${JAVAJARDIR:S,^${PREFIX}/,,}
@${RM} ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH}/bin/canu.defaults
do-install:
cd ${BUILD_WRKSRC}${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 ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_SHARE} "lib share" \
${STAGEDIR}${PREFIX}
.include <bsd.port.mk>
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