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This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.
46 lines
1.1 KiB
Makefile
46 lines
1.1 KiB
Makefile
PORTNAME= bbmap
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DISTVERSION= 38.90
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CATEGORIES= biology java
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MASTER_SITES= SF/bbmap/
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DISTNAME= BBMap_${PORTVERSION}
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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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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/license.txt
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RUN_DEPENDS= bash:shells/bash \
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pigz:archivers/pigz \
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pbzip2:archivers/pbzip2
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USES= shebangfix
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USE_JAVA= yes
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SHEBANG_FILES= ${WRKSRC}/*.sh
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WRKSRC= ${WRKDIR}/${PORTNAME}
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NO_BUILD= yes
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NO_ARCH= 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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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}${JAVAJARDIR}/bbmap
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.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh
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${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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