From nobody Fri Dec 06 14:39:24 2024 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Y4Ymr6pYwz5gN8L; Fri, 06 Dec 2024 14:39:24 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Y4Ymr6HP7z4F9P; Fri, 6 Dec 2024 14:39:24 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1733495964; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=g4nemGBHlk4UvsjYYn0CJ0fR2WsHDQBMyVolpd4uUGM=; b=AK2D0K2B8Bmt6iiRQjI+Ep1rhCw9nVJkQFNdzPSZ5afTw99NYyrVyzrSYPzfUCCV7Vaim2 W+u+HHdoXsLX7XC3+2AkvX0d18ind43bjmDGgnJ3x3XPYrUdPWlLO30lhpkGn7wsHT/olL 1uk5e3PoLjv9oY/+SxZLLrU7l6MT1WNyG8+ShLiLXVSr/N3sXhxy/R/Bgk8BQEnixz6DMs fCX/oNz0KB/gbRVur/jEUq/RwkCqMjqko83PaW+5gldZ1DbpeETIhG8/YLbpQJmnTnJjsA 0/6RrQdZisbAhWNnDf5PHsPrPeZhZdzun2ZOZdh0QAED01NL7eMdcqijxMSOMQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1733495964; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=g4nemGBHlk4UvsjYYn0CJ0fR2WsHDQBMyVolpd4uUGM=; b=bjAB/M9DXBYlfwXoD621g/jllyGg37rE2Msk++Dz91w/sWgsyjIxKv0dCOIX1tiNE4tdTF XJkye3COTDtlJjDZRPpeCQIsbrcaKCzG98pR7Ugj76QVeDsMI5swquujmtuh446ops6W4v 90MHD8Xtc5+8tM0UtWKwCRECVrFLjV91Xioa2RbFeW8BCoxX4qoSmoNcc4CZQzxdaNHHnl 4JyHv+AVc5Xn/IaSybag6idHRxq7pb3kg2crHS4t0t1DJav4DKU2jvDVL90K45/PHRpSjt +MaXsS1Ocfx80KKp/bCDKCsWrelZz/Jc1peQF86kJ6nAHikcsLe3j5+SuTMXaA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1733495964; a=rsa-sha256; cv=none; b=XVGgcs6tqoBUf9nKzNrrmj+EUdT52jugqVwG7BWdzDYF98y90bwStbpMuDoUPaBpiAZhOY tf4sygz6jzw6RTSnEA3zYgpjnZpcYMs7hkIGrZYnq6hESNC0v8YrI/nJnXvCWOk6a15NXb 9E5TZBpL8iJygvBTuAaZwJinlKDFbeWynoq/Nc75Y1JnaQDhBGNHbJsxNm4cwdNLHXZ6I2 kYwc8ZRTZa7srJ+T6sUacG7UQQvaC4fZSkYS5U6wHpkG1IKHQAvccOaudFm/qUoIuFm0IQ AjmuO7BJPrJdbrYaHqxDwdzGNtBphapJ1Tqufs6KwfZ4OfN/r8janF6RPA5B2g== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4Y4Ymr5m7VzhSs; Fri, 6 Dec 2024 14:39:24 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 4B6EdOVR095770; Fri, 6 Dec 2024 14:39:24 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4B6EdOw6095767; Fri, 6 Dec 2024 14:39:24 GMT (envelope-from git) Date: Fri, 6 Dec 2024 14:39:24 GMT Message-Id: <202412061439.4B6EdOw6095767@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 0e30cf43051d - main - biology/gemma: Update to 0.98.5 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 0e30cf43051d7834c2725311dd0724f088d9c8ea Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0e30cf43051d7834c2725311dd0724f088d9c8ea commit 0e30cf43051d7834c2725311dd0724f088d9c8ea Author: Jason W. Bacon AuthorDate: 2024-12-06 14:36:36 +0000 Commit: Jason W. Bacon 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.