From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id FJiROu8YqGDaCwEAgWs5BA (envelope-from ) for ; Fri, 21 May 2021 22:32:47 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id 4E6HNe8YqGClKAAAbx9fmQ (envelope-from ) for ; Fri, 21 May 2021 20:32:47 +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 8FF251A2BD for ; Fri, 21 May 2021 22:32:47 +0200 (CEST) Received: from localhost ([::1]:45110 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBp8-00030Z-LQ for larch@yhetil.org; Fri, 21 May 2021 16:32:46 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52468) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBke-0004af-G5 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54496) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBke-0002xq-8B for guix-patches@gnu.org; Fri, 21 May 2021 16:28:08 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBke-0000N1-51 for guix-patches@gnu.org; Fri, 21 May 2021 16:28:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 17/50] gnu: r-deseq: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:08 +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=B48575.16216288481052 (code B ref 48575); Fri, 21 May 2021 20:28:08 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:28 +0000 Received: from localhost ([127.0.0.1]:37731 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjz-0000Gn-Gj for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:27 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:38449) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjM-000094-Td for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:49 -0400 Received: by mail-wr1-f42.google.com with SMTP id j14so20456950wrq.5 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:26:48 -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=uS+iR7ArIs9A0QBxPdV6EFOExjvOpBKgBKACbdodBh4=; b=sOw+odoCzoPDXnzhuWNaEzq7yFsdQ+Cj8VIi+y9b1pDzuPa6dU+aR1HfAfMU273gvM YNCpg0jPX15+LYI4RJU5XDWb69pT3rHkK9waDlAGLlOutRa7TwkiVTGB398zv8FX9vQY VOzTrUoKNBIHgeokem0cC6lS9XZt5QcZhCmBA3eOe70g8P2638I/4nXxxyREeZ9WYk6y 6w2TgkQoGCTjjjWxx2XNqrkxSxCaVqVi1e+mN3OVIKRvavgn0InLk9fQlhT1pXCtK6dP 7hSKIqIvjG1htIms/8Nxk0Rv/BMJ15zfnGdb4KXtlR9Ocvcc7o/8zJeNNyBSbRa+c3JH dYug== 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=uS+iR7ArIs9A0QBxPdV6EFOExjvOpBKgBKACbdodBh4=; b=aQG5gvQxbYcUrBHdOQrMfLpkUoxy3W+H2fWzkBjeviQBPivHVIXtCHa5V5k6E/REsb PpguypDg2+IZWEqBSEDljSYL2BT4yYN+ZycFW7MF2kuzbsYZnskamb1C32gsbHq9F+pp wKsTdt+Oj24N6Tt8tx2zzuqwi9XeNC6GRvLiz4i959RqZIcbKm9xkGeVWm59Cr2mcXEI jIFdModh1/lIo+PxA6+ElakDg31+yqzm2APPK3pROfKm9pOh/UzbTgRnDPh/uOPttQBV RagIavgB54mUOAko+O7x98RQ3LPy/IR1EEmDjjQRTpAXqIzIhZhoURoWC0cGFFEFLF63 RGPA== X-Gm-Message-State: AOAM5305wIxFFAy7TEFMJFxGtUlf3lV66RD3xmEjjjXVqQbVfwok5mo7 CRohLxAR6XyxZK7PQkElgkNcp9oEpnY= X-Google-Smtp-Source: ABdhPJzoR7HKMFcpA9VYY094OO6TfCNo8L0KvfIeB94VKuy94E+lf10zpuxifvKu9wzyXTPo8lm2og== X-Received: by 2002:a5d:46c7:: with SMTP id g7mr11319126wrs.394.1621628803098; Fri, 21 May 2021 13:26:43 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:42 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:49 +0200 Message-Id: <20210521202622.26591-17-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=1621629167; 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=uS+iR7ArIs9A0QBxPdV6EFOExjvOpBKgBKACbdodBh4=; b=IUdvO621q7IJ7+CZ7J93ZyZmNi+BsRdwe7HmmbsnZz+QYhqL6BZFx1B0NRnAHrzVP7xx1I aTm+N9HVv91ko+iSvUpljCQRKrPjr7DGX1W4B6yrXNJu0ZvrjferFrkCDusSplOuUvfHAa mSa/A5zPArtylmuJJbtpJXNM78TWvJzaw0PPy7UB86MT2FhzHt5lqzM64kr1USnopBW/gC 4WJLohIDAUSd1sW+VN5TnEMVxCvcm6FlGpFyT+2iC8seCF/DwNE1fouXyMGPV6tjWdEpBB fDwyU96Vs8KxnUzkM/fa9CCldNY1ksRrmRXkRLXIFN9n13LuJSmTwpCZ1tHKmA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1621629167; a=rsa-sha256; cv=none; b=AQuz/4Z3rvXex81JuwsZ+92f0JggHqmIPvyAtPjm4LVmWdbmPbyehJ+9H8wRHoJBG429Dt RdvwoQnpspsOkttDuOhoQEaYRY/wEKGguircGizcTYQP2rKfExtBfm04hTYcdi6OZ5YJKD dqffwAfePJ6qI7ZWuFqGx8s7AjCEgDglAU2dgergVgriCtbyGjCJXl1yIaGjlBdBODi3e9 jCK2r6AvzGgyy99DOkk+n1hIzxEqEDd5dCdqJ9kGiPaufUKmVSqMSGYcFnU5/nj+cbstya o+x+6x1axTcOna+VVTjJLVCYwENFCFE5iQya9/J9Boe7SuLtbkhvhma28g3k7w== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=sOw+odoC; 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=sOw+odoC; 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: 8FF251A2BD X-Spam-Score: 2.66 X-Migadu-Scanner: scn0.migadu.com X-TUID: /d2+6xMKnwit * gnu/packages/bioinformatics.scm (r-deseq): Move from here... * gnu/packages/bioconductor.scm (r-deseq): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e58cd66fef..69ef513bc6 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2013,6 +2013,37 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-deseq + (package + (name "r-deseq") + (version "1.39.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq" version)) + (sha256 + (base32 + "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) + (properties `((upstream-name . "DESeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-lattice" ,r-lattice) + ("r-locfit" ,r-locfit) + ("r-mass" ,r-mass) + ("r-rcolorbrewer" ,r-rcolorbrewer))) + (home-page "https://www-huber.embl.de/users/anders/DESeq/") + (synopsis "Differential gene expression analysis") + (description + "This package provides tools for estimating variance-mean dependence in +count data from high-throughput genetic sequencing assays and for testing for +differential expression based on a model using the negative binomial +distribution.") + (license license:gpl3+))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c8444eea9f..2edb501f9b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) -(define-public r-deseq - (package - (name "r-deseq") - (version "1.39.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq" version)) - (sha256 - (base32 - "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) - (properties `((upstream-name . "DESeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "https://www-huber.embl.de/users/anders/DESeq/") - (synopsis "Differential gene expression analysis") - (description - "This package provides tools for estimating variance-mean dependence in -count data from high-throughput genetic sequencing assays and for testing for -differential expression based on a model using the negative binomial -distribution.") - (license license:gpl3+))) - (define-public r-edaseq (package (name "r-edaseq") -- 2.30.1