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PORTNAME= snpeff
DISTVERSION= 5.0
CATEGORIES= biology java python
MASTER_SITES= https://snpeff.blob.core.windows.net/versions/
DISTNAME= snpEff_latest_core
DIST_SUBDIR= ${PORTNAME}-${PORTVERSION}
MAINTAINER= jwb@FreeBSD.org
COMMENT= Genetic variant annotation and effect prediction toolbox
WWW= http://snpeff.sourceforge.net/
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE.md
RUN_DEPENDS= bash:shells/bash
USES= python:3.6+ shebangfix zip
USE_JAVA= yes
JAVA_VERSION= 17+
SHEBANG_FILES= scripts/* scripts/gsa/*
NO_BUILD= yes
NO_ARCH= yes
WRKSRC= ${WRKDIR}/snpEff
LIBEXEC_DIR= ${PREFIX}/libexec/snpeff
pre-configure:
${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
-e 's|%%JAVA_HOME%%|${JAVA_HOME}|g' \
${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift
do-install:
${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff
${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpEff ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpSift ${STAGEDIR}${PREFIX}/bin
${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/snpeff
${INSTALL_DATA} ${WRKSRC}/*.config ${STAGEDIR}${JAVAJARDIR}/snpeff
cd ${WRKSRC}/scripts && ${COPYTREE_BIN} . ${STAGEDIR}${LIBEXEC_DIR}
.include <bsd.port.mk>
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