From patchwork Mon Mar 15 13:01:34 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27708 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6715427BC55; Mon, 15 Mar 2021 13:03:56 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H3, RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 2134527BC54 for ; Mon, 15 Mar 2021 13:03:55 +0000 (GMT) Received: from localhost ([::1]:39308 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lLmt0-0003PG-Af for patchwork@mira.cbaines.net; Mon, 15 Mar 2021 09:03:54 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60042) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lLmsD-00032R-LR for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:51749) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lLmsC-0007Hz-4v for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:05 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lLmsC-0006Cb-2Y for guix-patches@gnu.org; Mon, 15 Mar 2021 09:03:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#47156] [PATCH 09/10] gnu: r-edger: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 15 Mar 2021 13:03:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47156 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47156@debbugs.gnu.org Cc: zimoun Received: via spool by 47156-submit@debbugs.gnu.org id=B47156.161581332823729 (code B ref 47156); Mon, 15 Mar 2021 13:03:04 +0000 Received: (at 47156) by debbugs.gnu.org; 15 Mar 2021 13:02:08 +0000 Received: from localhost ([127.0.0.1]:35055 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrI-0006Aa-0N for submit@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:08 -0400 Received: from mail-wm1-f51.google.com ([209.85.128.51]:37398) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lLmrB-00068Q-MX for 47156@debbugs.gnu.org; Mon, 15 Mar 2021 09:02:02 -0400 Received: by mail-wm1-f51.google.com with SMTP id f22-20020a7bc8d60000b029010c024a1407so20224467wml.2 for <47156@debbugs.gnu.org>; Mon, 15 Mar 2021 06:02:01 -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=934bcbrdffuahjUu3IX2GMxYkAsHi5dsEE/SASFznFA=; b=eOmH3tWGxGhlPyXeMLhBSP4+M1B5SPXFZwQzyTRhQqnnxXRIllCARGpjV9Bn7lHRCE 3t6lamyEUz2YmlLwWe5YlqglbqgMLGxWLdh08cWZpC5IYPdYQ35Vq4BPQaZXllYvEGRm 6j8QSN6lOHG5iTllzGpRYWUClE0GObMOVHE0jRoJJKK7oeZde/8n1XyoT40SoYpSle9F x87My3akfTwWry4swfvVR6AegnPwExd+1KBl6F4TqxULQ15WjWWztV7zMm6a3cNKOuX0 BKP6/GvsgBMlq8uD690YC+7EYHz82I8Xy1xu/j/WBNksX8L/ZFWPHFb6lsDgg3wWHYUp 152g== 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=934bcbrdffuahjUu3IX2GMxYkAsHi5dsEE/SASFznFA=; b=aQOhRime9aQkjtqcSf13sK6nonx5X6xCeWHr2E1rB+zjac3Voq8PLgTkd+h1EfUe+M lxOlWExuFWRe4hrdzINv3f79zDBD4Z5OiaCE6dQFRb4ODHO9OIRZ0cQNjSlremjI0AQi 6Va2HwvBpPHyWwSd1/0tDdVKJhVFXkestDllsDClhMHye+0yoKprHQhoK1hdM4ouM1gn /rS9lkdOmHeZGkfaoF7IjfWxOxjUUDAiAtW8Es5/4U9iNjwM7gHwS+LQcksXGTg4cV81 yv2KPTxrwDGDOCqF+k7ugGCPcAWCy8ohq2sgQ7K26mC5JCeFQkrcuu6+ZreG6q+kdftr Pfqw== X-Gm-Message-State: AOAM530gWfIzZJ8OzPMTBBLdLby4/DUl7IuIkWFA3vkkSw7lS71/XWsV AlxEtciuH8PM70zsawKOu1RmjXNmQng= X-Google-Smtp-Source: ABdhPJxNqZJFLO8INh+invR0Zxlhc3nWA7pckQds7udEiVKaAcd9DiptP7i45JaPgq81sc6U4Uf6Ww== X-Received: by 2002:a1c:400b:: with SMTP id n11mr25682401wma.167.1615813311169; Mon, 15 Mar 2021 06:01:51 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id f16sm18344646wrt.21.2021.03.15.06.01.50 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 15 Mar 2021 06:01:50 -0700 (PDT) From: zimoun Date: Mon, 15 Mar 2021 14:01:34 +0100 Message-Id: <20210315130134.30302-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210315130134.30302-1-zimon.toutoune@gmail.com> References: <20210315130134.30302-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (r-edger): Move from here... * gnu/packages/bioconductor.scm (r-edger): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4456d13c8..fb0127b7ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1684,6 +1684,34 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edger + (package + (name "r-edger") + (version "3.32.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "edgeR" version)) + (sha256 + (base32 + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) + (properties `((upstream-name . "edgeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-statmod" ,r-statmod))) ;for estimateDisp + (home-page "http://bioinf.wehi.edu.au/edgeR") + (synopsis "EdgeR does empirical analysis of digital gene expression data") + (description "This package can do differential expression analysis of +RNA-seq expression profiles with biological replication. It implements a range +of statistical methodology based on the negative binomial distributions, +including empirical Bayes estimation, exact tests, generalized linear models +and quasi-likelihood tests. It be applied to differential signal analysis of +other types of genomic data that produce counts, including ChIP-seq, SAGE and +CAGE.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6996011e..dc0d7a2906 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,34 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-edger - (package - (name "r-edger") - (version "3.32.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "edgeR" version)) - (sha256 - (base32 - "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) - (properties `((upstream-name . "edgeR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp - (home-page "http://bioinf.wehi.edu.au/edgeR") - (synopsis "EdgeR does empirical analysis of digital gene expression data") - (description "This package can do differential expression analysis of -RNA-seq expression profiles with biological replication. It implements a range -of statistical methodology based on the negative binomial distributions, -including empirical Bayes estimation, exact tests, generalized linear models -and quasi-likelihood tests. It be applied to differential signal analysis of -other types of genomic data that produce counts, including ChIP-seq, SAGE and -CAGE.") - (license license:gpl2+))) - (define-public r-variantannotation (package (name "r-variantannotation")