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# $NetBSD: Makefile,v 1.1 2021/05/26 19:13:39 brook Exp $
PKGNAME= beagle-5.2
CATEGORIES= biology
MASTER_SITES= https://faculty.washington.edu/browning/beagle/
DIST_SUBDIR= beagle-5.2
DISTFILES+= beagle.21Apr21.304.jar
DISTFILES+= bref3.21Apr21.304.jar
DISTFILES+= test.21Apr21.304.vcf.gz
MAINTAINER= pkgsrc-users@NetBSD.org
HOMEPAGE= https://faculty.washington.edu/browning/beagle/
COMMENT= Phasing genotypes and imputing ungenotyped markers
LICENSE= gnu-gpl-v3
WRKSRC= ${WRKDIR}
USE_LANGUAGES= # none
USE_JAVA= run
USE_TOOLS+= cut gzip tr
NO_BUILD= yes
SUBST_CLASSES+= prefix
SUBST_STAGE.prefix= pre-configure
SUBST_FILES.prefix= beagle.sh bref3.sh
SUBST_VARS.prefix+= PREFIX
SUBST_VARS.prefix+= JAVA_BINPREFIX
EGDIR= ${PREFIX}/share/examples/beagle
SUBST_CLASSES+= egdir
SUBST_STAGE.egdir= pre-configure
SUBST_FILES.egdir= beagle-example.sh
SUBST_VARS.egdir= EGDIR
INSTALLATION_DIRS+= bin libexec/beagle share/examples/beagle
do-extract:
${CP} ${DISTDIR}/${DIST_SUBDIR}/* ${WRKSRC}
post-extract:
${CP} ${FILESDIR}/beagle.sh ${WRKSRC}
${CP} ${FILESDIR}/beagle-example.sh ${WRKSRC}
${CP} ${FILESDIR}/bref3.sh ${WRKSRC}
${GZIP_CMD} -cd < ${WRKSRC}/test.21Apr21.304.vcf.gz \
| ${CUT} -f1-190 \
| ${TR} '/' '|' \
| ${GZIP_CMD} > ${WRKSRC}/ref.21Apr21.304.vcf.gz
${GZIP_CMD} -cd < ${WRKSRC}/test.21Apr21.304.vcf.gz \
| ${CUT} -f1-9,191-200 \
| ${GZIP_CMD} > ${WRKSRC}/target.21Apr21.304.vcf.gz
do-install:
${INSTALL_SCRIPT} ${WRKSRC}/beagle.sh ${DESTDIR}${PREFIX}/bin/beagle
${INSTALL_SCRIPT} ${WRKSRC}/bref3.sh ${DESTDIR}${PREFIX}/bin/bref3
${INSTALL_DATA} ${WRKSRC}/beagle.21Apr21.304.jar ${DESTDIR}${PREFIX}/libexec/beagle
${INSTALL_DATA} ${WRKSRC}/bref3.21Apr21.304.jar ${DESTDIR}${PREFIX}/libexec/beagle
${INSTALL_SCRIPT} ${WRKSRC}/beagle-example.sh ${DESTDIR}${PREFIX}/share/examples/beagle
${INSTALL_DATA} ${WRKSRC}/ref.21Apr21.304.vcf.gz ${DESTDIR}${PREFIX}/share/examples/beagle
${INSTALL_DATA} ${WRKSRC}/target.21Apr21.304.vcf.gz ${DESTDIR}${PREFIX}/share/examples/beagle
${INSTALL_DATA} ${WRKSRC}/test.21Apr21.304.vcf.gz ${DESTDIR}${PREFIX}/share/examples/beagle
.include "../../mk/java-vm.mk"
.include "../../mk/bsd.pkg.mk"
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