git: 0e30cf43051d - main - biology/gemma: Update to 0.98.5

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0e30cf43051d7834c2725311dd0724f088d9c8ea

commit 0e30cf43051d7834c2725311dd0724f088d9c8ea
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-12-06 14:36:36 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-12-06 14:36:36 +0000

    biology/gemma: Update to 0.98.5
    
    Several bug fixes and enhancements since 0.98.3
    Changes: https://github.com/genetics-statistics/GEMMA/releases
    
    PR:             283036
    Reported by:    alster@vinterdalen.se
---
 biology/gemma/Makefile  |  7 ++++---
 biology/gemma/distinfo  |  6 +++---
 biology/gemma/pkg-descr | 20 ++++++++++++++++++++
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/biology/gemma/Makefile b/biology/gemma/Makefile
index 855f3a86b669..6e1c6ef9c2b4 100644
--- a/biology/gemma/Makefile
+++ b/biology/gemma/Makefile
@@ -1,11 +1,12 @@
 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
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.