Attachment 255521 Details for Bug 283036 – [PATCH] biology/gemma: update 0.98.3 → 0.98.5

[patch] [PATCH] biology/gemma: update 0.98.3 → 0.98.5

0001-biology-gemma-update-0.98.3-0.98.5.patch (text/plain), 3.11 KB, created by Älven on 2024-11-29 07:32:31 UTC

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Creator: Älven

Created: 2024-11-29 07:32:31 UTC

Size: 3.11 KB

patch

obsolete

>From e4fb17aa59edf8594048969bd89acf4389863bd1 Mon Sep 17 00:00:00 2001
>From: Ãlven <alster@vinterdalen.se>
>Date: Fri, 29 Nov 2024 11:29:56 +0400
>Subject: [PATCH] biology/gemma: update 0.98.3 â 0.98.5
>MIME-Version: 1.0
>Content-Type: text/plain; charset=UTF-8
>Content-Transfer-Encoding: 8bit
>
>---
> 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.
>-- 
>2.47.1
>

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alster: maintainer-approval? (jwb)

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