diff --git a/biology/gemma/Makefile b/biology/gemma/Makefile index 855f3a86b669..6e1c6ef9c2b4 100644 --- a/biology/gemma/Makefile +++ b/biology/gemma/Makefile @@ -1,38 +1,39 @@ PORTNAME= gemma -DISTVERSION= 0.98.3 -PORTREVISION= 5 +DISTVERSIONPREFIX= v +DISTVERSION= 0.98.5 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Genome-wide Efficient Mixed Model Association -WWW= https://github.com/genetics-statistics/GEMMA +WWW= https://xiangzhou.github.io/software/ \ + https://github.com/genetics-statistics/GEMMA/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libgsl.so:math/gsl USES= blaslapack:openblas compiler:c++11-lang eigen:3 gmake \ localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= genetics-statistics GH_PROJECT= GEMMA MAKEFILE= ${FILESDIR}/Makefile # Assuming openblas is built with pthreads, not openmp CXXFLAGS+= -I${LOCALBASE}/include/eigen3 -DOPENBLAS -pthread LDFLAGS+= -lopenblas -pthread OPTIONS_DEFINE= EXAMPLES pre-configure: @${REINPLACE_CMD} -e 's|../bin/gemma|../gemma|' ${WRKSRC}/test/*.sh do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) do-test: (cd ${WRKSRC}/test && ${SH} test_suite.sh) .include diff --git a/biology/gemma/distinfo b/biology/gemma/distinfo index dde8eb92ac25..fd7346b8e723 100644 --- a/biology/gemma/distinfo +++ b/biology/gemma/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1609514940 -SHA256 (genetics-statistics-GEMMA-0.98.3_GH0.tar.gz) = 8c27874634269f52a194a41048e70c17e2128563f56bb8ef59338a93147c61ba -SIZE (genetics-statistics-GEMMA-0.98.3_GH0.tar.gz) = 49572695 +TIMESTAMP = 1732864105 +SHA256 (genetics-statistics-GEMMA-v0.98.5_GH0.tar.gz) = 3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677 +SIZE (genetics-statistics-GEMMA-v0.98.5_GH0.tar.gz) = 51259250 diff --git a/biology/gemma/pkg-descr b/biology/gemma/pkg-descr index 9db7086ea489..c4c81c9fa6f6 100644 --- a/biology/gemma/pkg-descr +++ b/biology/gemma/pkg-descr @@ -1,3 +1,23 @@ GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. + +Key features: + +1. Fast assocation tests implemented using the univariate linear mixed model + (LMM). In GWAS, this can correct for population structure and sample + non-exchangeability. It also provides estimates of the proportion of + variance in phenotypes explained by available genotypes (PVE), often called + "chip heritability" or "SNP heritability". +2. Fast association tests for multiple phenotypes implemented using a + multivariate linear mixed model (mvLMM). In GWAS, this can correct for + population structure and sample (non)exchangeability - jointly in multiple + complex phenotypes. +3. Bayesian sparse linear mixed model (BSLMM) for estimating PVE, phenotype + prediction, and multi-marker modeling in GWAS. +4. Estimation of variance components ("chip/SNP heritability") partitioned by + different SNP functional categories from raw (individual-level) data or + summary data. For raw data, HE regression or the REML AI algorithm can be + used to estimate variance components when individual-level data are + available. For summary data, GEMMA uses the MQS algorithm to estimate + variance components.