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| author | jwb <jwb@FreeBSD.org> | 2018-04-26 12:16:15 +0800 |
|---|---|---|
| committer | jwb <jwb@FreeBSD.org> | 2018-04-26 12:16:15 +0800 |
| commit | 28736c9cec5da62e63a4c0b2572a9fe7871b6ce1 (patch) | |
| tree | 8c402a8296cec715c4f3f7407728605f773527e7 /biology/canu/Makefile | |
| parent | ac2e8addabdb1baaf0b8fac8ab2c8bbee5767414 (diff) | |
| download | freebsd-ports-gnome-28736c9cec5da62e63a4c0b2572a9fe7871b6ce1.tar.gz freebsd-ports-gnome-28736c9cec5da62e63a4c0b2572a9fe7871b6ce1.tar.zst freebsd-ports-gnome-28736c9cec5da62e63a4c0b2572a9fe7871b6ce1.zip | |
biology/canu: Upgrade to 1.7 release
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D15201
Diffstat (limited to 'biology/canu/Makefile')
| -rw-r--r-- | biology/canu/Makefile | 45 |
1 files changed, 18 insertions, 27 deletions
diff --git a/biology/canu/Makefile b/biology/canu/Makefile index fdfbb42faf97..19ab1b85b2fb 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,16 +1,15 @@ # $FreeBSD$ -PORTNAME= canu +PORTNAME= canu DISTVERSIONPREFIX= v -DISTVERSION= 1.6 -PORTREVISION= 3 -CATEGORIES= biology java perl5 +DISTVERSION= 1.7 +CATEGORIES= biology java perl5 MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler LICENSE= GPLv2 -LICENSE_FILE= ${WRKSRC}/README.license.GPL +LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL LIB_DEPENDS= libboost_regex.so:devel/boost-libs RUN_DEPENDS= gnuplot:math/gnuplot @@ -19,14 +18,12 @@ 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 - +WRKSRC_SUBDIR= src # Makefile compiles directly into ${DESTDIR}${PREFIX} -MAKE_ENV+= DESTDIR=${BUILD_WRKSRC} +MAKE_ENV+= DESTDIR=${WRKSRC} post-patch: ${REINPLACE_CMD} \ @@ -34,33 +31,27 @@ post-patch: -e 's|-funroll-loops||g' \ -e 's|-fexpensive-optimizations||g' \ -e 's|amd64|${ARCH}|g' \ - ${BUILD_WRKSRC}/Makefile + ${WRKSRC}/Makefile ${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \ - ${BUILD_WRKSRC}/pipelines/canu/OverlapMhap.pm + ${WRKSRC}/pipelines/canu/OverlapMhap.pm ${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \ - ${BUILD_WRKSRC}/pipelines/canu.pl + ${WRKSRC}/pipelines/canu.pl -# Reorganize according to filesystem hierarchy standard +# Upstream does not want to use lib/perl5/site_perl post-build: - @${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 + ${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5 + ${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \ + ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5 do-install: - cd ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_BIN} bin \ - ${STAGEDIR}${PREFIX} + ${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 ${BUILD_WRKSRC}${PREFIX}/FreeBSD-${ARCH} && ${COPYTREE_SHARE} "lib share" \ - ${STAGEDIR}${PREFIX} + (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \ + ${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX}) .include <bsd.port.mk> |