Index: head/biology/canu/Makefile =================================================================== --- head/biology/canu/Makefile (revision 456981) +++ head/biology/canu/Makefile (revision 456982) @@ -1,65 +1,65 @@ # $FreeBSD$ PORTNAME= canu DISTVERSIONPREFIX= v DISTVERSION= 1.6 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 +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