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