PORTNAME= bcf-score
DISTVERSION= 1.20
PORTREVISION= 3
CATEGORIES= biology
MASTER_SITES= https://software.broadinstitute.org/software/score/
# Get this right, or ports will download bcftools in it's place via tuple
DISTFILES+= score_${DISTVERSION}-20240505.tar.gz
MAINTAINER= [email protected]
COMMENT= Bcftools plugins for GWAS-VCF summary statistics files
WWW= https://software.broadinstitute.org/software/score/
LICENSE= MIT
BUILD_DEPENDS= htslib>=1.22:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib libcholmod.so:math/suitesparse-cholmod
TEST_DEPENDS= bash:shells/bash
RUN_DEPENDS= bash:shells/bash bcftools>=${PORTVERSION}:biology/bcftools
USES= autoreconf gmake localbase perl5 python:env shebangfix
USE_GITHUB= yes
USE_PERL5= test
GH_ACCOUNT= samtools
GH_PROJECT= bcftools
GH_TAGNAME= 1.22
GNU_CONFIGURE= yes
SHEBANG_FILES= misc/* test/test.pl
# From pgs.mk
CFLAGS+= -isystem ${LOCALBASE}/include/suitesparse
LDFLAGS+= -lcholmod
pre-configure:
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
${WRKSRC}/configure.ac
post-extract:
@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
@${MKDIR} ${WRKSRC}/bcf-score
@${CP} ${WRKDIR}/*.R ${WRKSRC}/bcf-score
# One .so for each .c in the score distfile
do-install:
${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/blup.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/liftover.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/metal.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/munge.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/pgs.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/score.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
(cd ${WRKSRC}/bcf-score && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
.include <bsd.port.mk>
