diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 72a628226299..47880cd12b4c 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,66 +1,66 @@ PORTNAME= canu DISTVERSION= 2.2 -CATEGORIES= wip biology java perl5 +CATEGORIES= biology java perl5 # Github auto-generated tarballs lack submodules MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/ MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler 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 localbase perl5 tar:xz 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 .include # 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 ${WRKSRC}/utility/src/parasail/cpuid.c .endif pre-configure: @${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