74 lines
2.2 KiB
Makefile
74 lines
2.2 KiB
Makefile
# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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# Sun May 1 07:19:47 CDT 2016 #
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###########################################################
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# Test new versions with Trinity before upgrading
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#DISTVERSIONPREFIX= v
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DISTNAME= rsem-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=deweylab/}
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GITHUB_PROJECT= RSEM
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GITHUB_TAG= v${PORTVERSION}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://deweylab.biostat.wisc.edu/rsem/README.html
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COMMENT= RNA-Seq by Expectation-Maximization
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LICENSE= gnu-gpl-v3
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# Test and change if necessary.
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# MAKE_JOBS_SAFE= no
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USE_LANGUAGES= c c++
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# Gmake is for bundled samtools, which contains modifications for rsem.
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# Should be unbundled in the future.
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USE_TOOLS+= gmake perl:run
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REPLACE_PERL= convert-sam-for-rsem \
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extract-transcript-to-gene-map-from-trinity \
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rsem-calculate-expression \
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rsem-control-fdr \
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rsem-generate-data-matrix \
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rsem-generate-ngvector \
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rsem-plot-transcript-wiggles \
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rsem-prepare-reference \
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rsem-run-ebseq \
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rsem_perl_utils.pm
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REPLACE_PYTHON= rsem-refseq-extract-primary-assembly \
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rsem-gff3-to-gtf
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SUBST_CLASSES+= rscript
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SUBST_STAGE.rscript= post-patch
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SUBST_SED.rscript= -e "s|\#!/usr/bin/env Rscript|${PREFIX}/bin/Rscript|g"
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SUBST_FILES.rscript= rsem-gen-transcript-plots \
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rsem-plot-model
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SUBST_CLASSES+= siteperl
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SUBST_STAGE.siteperl= post-patch
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SUBST_SED.siteperl+= -e 's|use lib $$FindBin::RealBin|use lib "${SITE_PERL}"|'
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SUBST_FILES.siteperl+= ${WRKSRC}/rsem*
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# Make sure all rsem programs use libexec/rsem/samtools
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SUBST_CLASSES+= samdir
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SUBST_STAGE.samdir= post-patch
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SUBST_SED.samdir+= -e 's|samtools|${PREFIX}/libexec/rsem/samtools|g'
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SUBST_FILES.samdir+= ${WRKSRC}/rsem-calculate-expression
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SUBST_FILES.samdir+= ${WRKSRC}/rsem-plot-transcript-wiggles
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WRKSRC= ${WRKDIR}/RSEM-${PORTVERSION}
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MAKE_ENV= libexecdir=${PREFIX}/libexec \
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perl_mod_dir=${SITE_PERL}
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PORTVERSION= 1.2.30
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SITE_PERL= ${PREFIX}/share/rsem
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post-install:
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${RM} -rf ${DESTDIR}${PREFIX}/bin/samtools-*
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.include "../../math/R/buildlink3.mk"
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.include "../../lang/python/application.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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