mirror of
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43 lines
1.2 KiB
Makefile
43 lines
1.2 KiB
Makefile
PORTNAME= snpeff
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DISTVERSION= 5.0
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CATEGORIES= biology java python
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MASTER_SITES= https://snpeff.blob.core.windows.net/versions/
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DISTNAME= snpEff_latest_core
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DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Genetic variant annotation and effect prediction toolbox
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LICENSE= MIT
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LICENSE_FILE= ${WRKSRC}/LICENSE.md
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RUN_DEPENDS= bash:shells/bash
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USES= python:3.6+ shebangfix zip
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USE_JAVA= yes
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JAVA_VERSION= 12+
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SHEBANG_FILES= scripts/* scripts/gsa/*
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NO_BUILD= yes
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NO_ARCH= yes
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WRKSRC= ${WRKDIR}/snpEff
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LIBEXEC_DIR= ${PREFIX}/libexec/snpeff
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pre-configure:
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${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
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-e 's|%%JAVA_HOME%%|${JAVA_HOME}|g' \
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${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift
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do-install:
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${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff
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${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
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${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpEff ${STAGEDIR}${PREFIX}/bin
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${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpSift ${STAGEDIR}${PREFIX}/bin
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${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/snpeff
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${INSTALL_DATA} ${WRKSRC}/*.config ${STAGEDIR}${JAVAJARDIR}/snpeff
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cd ${WRKSRC}/scripts && ${COPYTREE_BIN} . ${STAGEDIR}${LIBEXEC_DIR}
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.include <bsd.port.mk>
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