68 lines
1.8 KiB
Makefile
68 lines
1.8 KiB
Makefile
# $FreeBSD$
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PORTNAME= dDocent
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DISTVERSIONPREFIX= v
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DISTVERSION= 2.2.25
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CATEGORIES= biology java
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Bash pipeline for RAD sequencing
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LICENSE= MIT
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# ddocent test data do not unpack with FreeBSD 11.1 /usr/bin/unzip
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RUN_DEPENDS= unzip>=0:archivers/unzip \
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mawk>=0:lang/mawk \
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gawk>=0:lang/gawk \
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coreutils>=0:sysutils/coreutils \
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gnuplot>=0:math/gnuplot \
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parallel>=0:sysutils/parallel \
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bash:shells/bash \
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bwa>=0.7.13:biology/bwa \
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cd-hit>=0:biology/cd-hit \
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samtools>=1.3:biology/samtools \
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vcftools>=0.1.15:biology/vcftools \
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trimmomatic>=0:biology/trimmomatic \
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bamtools>=0:biology/bamtools \
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stacks>=0:biology/stacks \
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rainbow>=0:biology/rainbow \
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trimadap>=0:biology/trimadap \
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seqtk>=0:biology/seqtk \
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bedtools>=2.26.0:biology/bedtools \
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pear-merger>=0:biology/pear-merger \
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vcflib>=0:biology/vcflib \
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freebayes:biology/freebayes
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USES= perl5 python shebangfix
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SHEBANG_FILES= dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
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USE_JAVA= yes
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USE_GITHUB= yes
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GH_ACCOUNT= jpuritz
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NO_BUILD= yes
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NO_ARCH= yes
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# These are on top of patch-dDocent, so don't apply them within the source
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# tree, or they'll get picked up by patch generators, and hard-code PREFIX.
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post-install:
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${REINPLACE_CMD} -i '' \
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-e 's|%%PREFIX%%|${PREFIX}|g' \
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-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
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-e 's|%%BASH%%|${LOCALBASE}/bin/bash|g' \
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-e 's|python|${PYTHON_CMD}|g' \
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${STAGEDIR}${PREFIX}/bin/dDocent
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do-install:
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${MKDIR} ${STAGEDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} \
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${WRKSRC}/dDocent \
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${WRKSRC}/*.sh \
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${FILESDIR}/ddocent-assembly-test \
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${FILESDIR}/ddocent-assembly-test-cleanup \
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${WRKSRC}/scripts/*.sh \
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${WRKSRC}/scripts/*.pl \
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${WRKSRC}/scripts/dDocent_filters \
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${STAGEDIR}${PREFIX}/bin
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.include <bsd.port.mk>
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