84 lines
2.8 KiB
Makefile
84 lines
2.8 KiB
Makefile
# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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# Thu Mar 22 18:28:27 CDT 2018 #
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###########################################################
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DISTNAME= dDocent-${PORTVERSION}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=jpuritz/}
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GITHUB_PROJECT= dDocent
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GITHUB_TAG= v${PORTVERSION}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://ddocent.com/
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COMMENT= Bash pipeline for RAD sequencing
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LICENSE= mit
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# bedtools version: https://github.com/jpuritz/dDocent/issues/15
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# New ddocent works with 2.23.0 or >= 2.26.0
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# Do we really need trimadap? It used to be part of seqtk.
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# ddocent test data do not unpack with FreeBSD 11.1 /usr/bin/unzip
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DEPENDS= mawk>=0:../../lang/mawk
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DEPENDS+= gawk>=0:../../lang/gawk
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DEPENDS+= coreutils>=0:../../sysutils/coreutils
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DEPENDS+= gnuplot>=0:../../graphics/gnuplot
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DEPENDS+= parallel>=0:../../parallel/parallel
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DEPENDS+= bwa>=0.7.13:../../biology/bwa
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DEPENDS+= cdhit>=0:../../biology/cdhit
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DEPENDS+= samtools>=1.3:../../biology/samtools
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DEPENDS+= vcftools>=0.1.15:../../wip/vcftools
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DEPENDS+= Trimmomatic>=0:../../biology/trimmomatic
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DEPENDS+= stacks>=0:../../biology/stacks
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DEPENDS+= rainbow>=0:../../wip/rainbow
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DEPENDS+= trimadap>=0:../../wip/trimadap
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DEPENDS+= seqtk>=0:../../wip/seqtk
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DEPENDS+= bedtools2>=2.26.0:../../wip/bedtools2
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DEPENDS+= pear-merger>=0:../../wip/pear-merger
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DEPENDS+= freebayes>=0:../../wip/freebayes
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## These follow patch-dDocent, so don't apply them within the source tree,
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## or they'll get picked up by patch generators and hard-code PREFIX
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SUBST_CLASSES+= prefix
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SUBST_STAGE.prefix= post-install
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SUBST_SED.prefix+= -e 's|%%PREFIX%%|${PREFIX}|g'
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SUBST_SED.prefix+= -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g'
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SUBST_SED.prefix+= -e 's|python|${PYTHONBIN}|g'
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SUBST_FILES.prefix+= ${DESTDIR}${PREFIX}/bin/dDocent
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USE_LANGUAGES= # none
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REPLACE_BASH= dDocent *.sh
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REPLACE_BASH+= scripts/ddocent-assembly-test* scripts/*.sh scripts/dDocent_filters
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REPLACE_PERL= scripts/*.pl
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REPLACE_PYTHON= scripts/*.py
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NO_BUILD= yes
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USE_TOOLS= bash perl unzip
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ERROR: [check-interpreter.mk] The interpreter "/usr/bin/env" of "/usr/pkgsrc/wip/ddocent/work/.destdir/usr/pkg/bin/ddocent-test" is not allowed.
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PORTVERSION= 2.5.2
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JAVAJARDIR= ${PREFIX}/lib/java
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INSTALLATION_DIRS= bin
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post-extract:
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${CP} ${FILESDIR}/ddocent-assembly-test ${FILESDIR}/ddocent-assembly-test-cleanup \
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${WRKSRC}/scripts
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do-install:
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${INSTALL_SCRIPT} \
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${WRKSRC}/dDocent \
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${WRKSRC}/*.sh \
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${WRKSRC}/scripts/ddocent-assembly-test \
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${WRKSRC}/scripts/ddocent-assembly-test-cleanup \
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${WRKSRC}/scripts/*.sh \
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${WRKSRC}/scripts/*.pl \
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${WRKSRC}/scripts/dDocent_filters \
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${DESTDIR}${PREFIX}/bin
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.include "../../lang/python/tool.mk"
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.include "../../wip/vcflib/buildlink3.mk"
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.include "../../wip/bamtools/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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