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# $NetBSD: Makefile,v 1.4 2019/08/11 13:17:59 wiz Exp $
DISTNAME= canu-1.8
PKGREVISION= 2
CATEGORIES= biology java
MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
GITHUB_TAG= v${PKGVERSION_NOREV}
MAINTAINER= bacon@NetBSD.org
HOMEPAGE= https://canu.readthedocs.io/
COMMENT= Single molecule sequence assembler for genomes large and small
LICENSE= gnu-gpl-v2
DEPENDS+= gnuplot>0:../../graphics/gnuplot
# Makefile compiles directly into ${DESTDIR}${PREFIX}
SUBST_CLASSES+= optimize
SUBST_STAGE.optimize= pre-configure
SUBST_SED.optimize+= -e 's|-g3||g'
SUBST_SED.optimize+= -e 's|-O3||g'
SUBST_SED.optimize+= -e 's|-O4||g'
SUBST_SED.optimize+= -e 's|-funroll-loops||g'
SUBST_SED.optimize+= -e 's|-fexpensive-optimizations||g'
SUBST_SED.optimize+= -e 's|-finline-functions||g'
SUBST_FILES.optimize+= ${WRKSRC}/Makefile
SUBST_CLASSES+= jar
SUBST_STAGE.jar= pre-configure
SUBST_SED.jar+= -e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g'
SUBST_FILES.jar+= ${WRKSRC}/pipelines/canu/OverlapMhap.pm
SUBST_CLASSES+= perl
SUBST_STAGE.perl= pre-configure
SUBST_SED.perl+= -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g'
SUBST_FILES.perl+= ${WRKSRC}/pipelines/canu.pl
REPLACE_PERL+= bogart/*.pl
REPLACE_PERL+= pipelines/*.pl
REPLACE_PERL+= bogus/*.pl
REPLACE_PERL+= bogart-analysis/*.pl
REPLACE_PERL+= overlapBasedTrimming/*.pl
REPLACE_PERL+= overlapInCore-analysis/*.pl
REPLACE_PERL+= merTrim/*.pl
REPLACE_PERL+= erateEstimate/*.pl
REPLACE_PERL+= meryl/.pl
REPLACE_PERL+= fastq-utilities/*.pl
REPLACE_PERL+= *.pl
# May work on other 64-bit processors, but untested
ONLY_FOR_PLATFORM= *-*-x86_64
USE_LANGUAGES= c c++
USE_JAVA= run
USE_JAVA2= 8
USE_TOOLS+= gmake pax perl
GCC_REQD+= 4.8
WRKSRC= ${WRKDIR}/canu-${PKGVERSION_NOREV}/src
MAKE_ENV+= DESTDIR=${WRKSRC}
TMP_INST= ${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
SITE_PERL_REL= lib/perl5/site_perl
JAVAJARDIR= share/java/classes
INSTALLATION_DIRS= bin ${JAVAJARDIR}
post-extract:
${CHMOD} -R g-w ${WRKDIR}
post-build:
${MKDIR} ${TMP_INST}/lib/perl5
${MV} ${TMP_INST}/lib/site_perl ${TMP_INST}/lib/perl5
${RM} -f ${TMP_INST}/bin/canu.defaults
do-install:
cd ${TMP_INST}/bin && ${PAX} -wr * ${DESTDIR}${PREFIX}/bin
cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5
cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
.include "../../devel/boost-libs/buildlink3.mk"
.include "../../lang/perl5/module.mk"
.include "../../mk/bsd.pkg.mk"
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