From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id WIcnNSwZqGAYBQEAgWs5BA (envelope-from ) for ; Fri, 21 May 2021 22:33:48 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id OIXfMCwZqGBQQQAA1q6Kng (envelope-from ) for ; Fri, 21 May 2021 20:33:48 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 433352204F for ; Fri, 21 May 2021 22:33:48 +0200 (CEST) Received: from localhost ([::1]:47560 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBq7-0004ki-9L for larch@yhetil.org; Fri, 21 May 2021 16:33:47 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52646) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkp-0005Nu-U2 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:19 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54525) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkp-00034Y-Ml for guix-patches@gnu.org; Fri, 21 May 2021 16:28:19 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkp-0000QT-JK for guix-patches@gnu.org; Fri, 21 May 2021 16:28:19 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:19 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48575 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 48575@debbugs.gnu.org. Cc: zimoun Received: via spool by 48575-submit@debbugs.gnu.org id=B48575.16216288631273 (code B ref 48575); Fri, 21 May 2021 20:28:19 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:43 +0000 Received: from localhost ([127.0.0.1]:37789 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBkE-0000KL-MF for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:43 -0400 Received: from mail-wr1-f54.google.com ([209.85.221.54]:42601) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjc-0000Cz-HM for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:10 -0400 Received: by mail-wr1-f54.google.com with SMTP id x8so22193819wrq.9 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:04 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=WTJ0QKwfkRwMUejAmpqr+O0CLj6EkllRvJX9rei3i0w=; b=WKFR21DO7KlMgwuCIOVQDFbiHZxqRr0lEKp4SNxLGF7K5JZqbJA8XJpLSzOg7yzGzF n/e0Jx3WbWODAWKzPT7UcyITg7Sc9Pz1aR+e9vZ0QqpAoZhvz/ByGEjPGZ/IDAyiQaAQ VLbUE/iIxQhkFrmVC1PoZO5UySSQJUEEJtgo/4n4TNBDqqeD/S6p9mjycoC7HP+0YeFm tgk9o83HGvLQGITc7VTIzDskTEB7ONigU+niH3rCewvx9FG96X0zDt05f79ZMYfXd/VJ eVH2CWZnZQsluBZ79MSnORJkocCDc7VFhkfFZ568SPHu9uIW0C1Wyhbcu5IOTQpPUFOa KyTw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=WTJ0QKwfkRwMUejAmpqr+O0CLj6EkllRvJX9rei3i0w=; b=nyfh4GEkbhgyTDYQMPJ4O7DmCNf680coJMTgttt6k6D2vycrFXsMs5LUxjnvUHggXw iiQtM1VhpGROn8FCY8SPxtk7pme1Hgsp2Awr8Dx2ADMZ5xkz4XSQuVSdmEk0ipmsuOQt YGIeoiTanzNnAO5PJB3WKfyzKvrbYiYWabV2QvoYSdxcnDTcbpkyyutXX10hdbFOGHfu GbeHHkoFIhqPrwkubtbWdFSe6mT7thKCh8WYncOwufH2nHeXby2s8BgBYz+/6d1oOjdg bgMQOjDlJTNA7Iew5LJBgQRROca+8SGdqb/u+hTmJvPDpohQGDLa1AYUNNLFPYs9d+YU ckuQ== X-Gm-Message-State: AOAM533b2cKJCuHehYyK2RAu/eaP60hdaZVFuMATc+G7Ze2OMosmpKz0 cuDMBMz6XTun2/tFkibjC3/8AlaPsjI= X-Google-Smtp-Source: ABdhPJzB4ffS4QtsmsD1u+kMcy9Jgjw1AMyvbz/ESowmgd0cX5z3uoLFn1kLjimE1hoXZfoTcIjjTQ== X-Received: by 2002:a5d:5052:: with SMTP id h18mr11082812wrt.365.1621628817984; Fri, 21 May 2021 13:26:57 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.57 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:57 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:22 +0200 Message-Id: <20210521202622.26591-50-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210521202622.26591-1-zimon.toutoune@gmail.com> References: <20210521202622.26591-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1621629228; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=WTJ0QKwfkRwMUejAmpqr+O0CLj6EkllRvJX9rei3i0w=; b=MtR0O4iUJ8ZpRwz/laXRfpLP6yqYNLwJoa0GhiF7NmEtFwi6sKKxymvh4oXQIRxmGsonoZ hx+G579NmdeYdpSB2B0XgFVOQpNy87wFKjVFGys/YvJcw2Hu+AhEIuaEb00FbDJmijjLxJ AGvyU4JBPgNKMXGRSvU5QlaphzXz76c9OMLgrFva3p+Jzgs8XTyJI8ZP7J2rRLLQtTmqHw P5TFY4APNoa82syRRg7YcBJ5y0Ya7sGOPg4Zz4JzzEDG7DF1mFNVpdP6yXdOVAVrUhBSK8 Q8L827erfvWVC0Wkckvo1QSgS8I9nTytlQ5On+Vi5HeMGdq35MtTyp8YMU4vjA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1621629228; a=rsa-sha256; cv=none; b=l/ckeBxR0fy6W0GQdKV8lfKf+hGnWDc8dSKNx2BecBvv3Bcoh4Ts108zS/OCJ4kNjbzXp3 KUJFPgNzH0gxMi/S9UIbMWcsw/bdtKv8bupI1rkJYg5iQ85KJ8Hn0v87qSEF6XrVPYwKZz 4YJDzLMt1dfH8qA/0vYNbB+I/go6NjIghSnURejyiLPAo1DqxcGX5vU0/JlCPjVw1mnycQ blPkYJCIK7CWPk+dKErMVUJYdeXTwMSm3HTs9oYt1jSLLjf6ck+Kn+Rku7yUGAtfQ6kBHl qZ2zqfAyL5WjMO51uhbTHvlh7sh6nERBD/vplYxQli4H4LW0Aqpq3J1dbD1AVw== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=WKFR21DO; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 2.66 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=WKFR21DO; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 433352204F X-Spam-Score: 2.66 X-Migadu-Scanner: scn0.migadu.com X-TUID: rRjf1P8p07tm * gnu/packages/bioinformatics.scm (r-methylkit): Move from here... * gnu/packages/bioconductor.scm (r-methylkit): ...to here. --- gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 47 --------------------------------- 2 files changed, 47 insertions(+), 47 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fe91fd486f..54a6afcf3d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3102,6 +3102,53 @@ and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) +(define-public r-methylkit + (package + (name "r-methylkit") + (version "1.16.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "methylKit" version)) + (sha256 + (base32 + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) + (properties `((upstream-name . "methylKit"))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-emdbook" ,r-emdbook) + ("r-fastseg" ,r-fastseg) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-iranges" ,r-iranges) + ("r-kernsmooth" ,r-kernsmooth) + ("r-limma" ,r-limma) + ("r-mclust" ,r-mclust) + ("r-mgcv" ,r-mgcv) + ("r-qvalue" ,r-qvalue) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-zlibbioc" ,r-zlibbioc))) + (native-inputs + `(("r-knitr" ,r-knitr))) ; for vignettes + (home-page "https://github.com/al2na/methylKit") + (synopsis + "DNA methylation analysis from high-throughput bisulfite sequencing results") + (description + "MethylKit is an R package for DNA methylation analysis and annotation +from high-throughput bisulfite sequencing. The package is designed to deal +with sequencing data from @dfn{Reduced representation bisulfite +sequencing} (RRBS) and its variants, but also target-capture methods and whole +genome bisulfite sequencing. It also has functions to analyze base-pair +resolution 5hmC data from experimental protocols such as oxBS-Seq and +TAB-Seq.") + (license license:artistic2.0))) + (define-public r-motifrg (package (name "r-motifrg") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79146f915f..48b521f755 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8312,53 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) -(define-public r-methylkit - (package - (name "r-methylkit") - (version "1.16.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "methylKit" version)) - (sha256 - (base32 - "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) - (properties `((upstream-name . "methylKit"))) - (build-system r-build-system) - (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes - (home-page "https://github.com/al2na/methylKit") - (synopsis - "DNA methylation analysis from high-throughput bisulfite sequencing results") - (description - "MethylKit is an R package for DNA methylation analysis and annotation -from high-throughput bisulfite sequencing. The package is designed to deal -with sequencing data from @dfn{Reduced representation bisulfite -sequencing} (RRBS) and its variants, but also target-capture methods and whole -genome bisulfite sequencing. It also has functions to analyze base-pair -resolution 5hmC data from experimental protocols such as oxBS-Seq and -TAB-Seq.") - (license license:artistic2.0))) - (define-public r-raremetals2 (package (name "r-raremetals2") -- 2.30.1