53 lines
1.4 KiB
Makefile
53 lines
1.4 KiB
Makefile
PORTNAME= bbmap
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DISTVERSIONPREFIX= v
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DISTVERSION= 40.02
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CATEGORIES= biology java
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= BBMap short read aligner, and other bioinformatic tools
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WWW= https://jgi.doe.gov/data-and-tools/bbtools/ \
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https://sourceforge.net/projects/bbmap/ \
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https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/license.txt
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RUN_DEPENDS= bash:shells/bash \
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pbzip2:archivers/pbzip2 \
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pigz:archivers/pigz
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USES= java shebangfix
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USE_GITHUB= yes
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GH_ACCOUNT= bbushnell
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GH_PROJECT= BBTools
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SHEBANG_FILES= ${WRKSRC}/*.sh
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NO_ARCH= yes
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NO_BUILD= yes
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LIBEXEC_DIR= ${PREFIX}/libexec/bbmap
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pre-configure:
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${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \
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${WRKSRC}/*.sh
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${REINPLACE_CMD} \
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-e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \
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${WRKSRC}/*.sh
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# FIXME: Find out which scripts are meant to be part of the CLI
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do-install:
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@${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
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@${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap
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${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR}
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cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \
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${STAGEDIR}${JAVAJARDIR}/bbmap
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.for f in bbmap.sh bbduk.sh bbmerge.sh bbnorm.sh tadpole.sh clumpify.sh \
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callvariants.sh bbsplit.sh sendsketch.sh comparesketch.sh \
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dedupe.sh bbmap.sh bloomfilter.sh reformat.sh \
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bbmerge.sh tadpole.sh bbversion.sh
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${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin
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.endfor
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.include <bsd.port.mk>
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