From patchwork Mon Mar 8 17:57:56 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 27545 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 0C6EE27BC50; Mon, 8 Mar 2021 18:54:37 +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 B812527BC52 for ; Mon, 8 Mar 2021 18:54:34 +0000 (GMT) Received: from localhost ([::1]:46876 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lJL1V-0001SI-Re for patchwork@mira.cbaines.net; Mon, 08 Mar 2021 13:54:33 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:59068) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lJK9r-0003qO-Q1 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:33233) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lJK9m-0001Jb-Qp for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lJK9m-0002hU-Q1 for guix-patches@gnu.org; Mon, 08 Mar 2021 12:59:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#47010] [PATCH 03/10] gnu: r-dexseq: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Mar 2021 17:59:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 47010 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 47010@debbugs.gnu.org Cc: zimoun Received: via spool by 47010-submit@debbugs.gnu.org id=B47010.161522630710261 (code B ref 47010); Mon, 08 Mar 2021 17:59:02 +0000 Received: (at 47010) by debbugs.gnu.org; 8 Mar 2021 17:58:27 +0000 Received: from localhost ([127.0.0.1]:44761 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK9D-0002fP-GB for submit@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:27 -0500 Received: from mail-wr1-f47.google.com ([209.85.221.47]:46781) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lJK99-0002e5-1b for 47010@debbugs.gnu.org; Mon, 08 Mar 2021 12:58:23 -0500 Received: by mail-wr1-f47.google.com with SMTP id a18so12368403wrc.13 for <47010@debbugs.gnu.org>; Mon, 08 Mar 2021 09:58:22 -0800 (PST) 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=i/9dtr60p5NUJjnBPgAH6JZTQEqskEyPpFovnlma3oM=; b=b/AeF79Febdp+9x3kXAsGr2/tQN+FXg2/JseOLdvCb7kCsabj/8ZI+86w7AX1Avt25 47NnGDOJmq5C7yM+iPojfZXH5VE5WHTUEqNXXHyBzGSg0YreqvNLh1WpeH0PNNXTLez2 2uz/jkSk+ggy+d6h2sBbLD/Xyaa33seNlfZCs4OZMquNVC+e6dZbV4klc/v/mgj1BgXt ERIkLTK24EcC1AUk++fisEv2mJXGCW6fwgUqjLHBiwzyeg/iF3r7BGxmlryMPzEIP31X N9AW+Ml7k7LAaYxLeQzLjYvX7G2g/OoJJ5KCe+rDA7M2ZiESiLrwKS9Aix9Flfmf7TSu WDzg== 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=i/9dtr60p5NUJjnBPgAH6JZTQEqskEyPpFovnlma3oM=; b=B41zQSxmoeeCiC+2Y+W4Mp03lAkvjYmNWpB4zRbq3PTh4eLVo/MIu4Gx00scWr2dwp wu36/pbJI7H+F05PDmaCNoiZhKgYfuKQsS6dwM+IzpfPduPPfoCMj1iJdXYGvViv2x0t 3w/lffjkLLygzI1nfwsP5oGbE8XtGlU1FxgWAQMxmR2egZ0lSNmCNoTdrjAr3yqkRkK7 zmT/nf9RH0H9X6rhpL8gUSr1o2i61oV9g32Hqr6maM2EcQMeWHwT8JoLGp/XMv985q6s svziahisAk4uY+FQiEKl0/Db9mF/0ChXKzo94eu2hfyRdQNb1KUhDQ+SYoIJqOW+BHlg sPiA== X-Gm-Message-State: AOAM532SOtUUZfQzO3uRTMQhrL2EuvplDnZhpxtLoplC2H4dDRXNTw7G DMm8rHxe7fhPSHCeiNGVO/IsC5zE0t0= X-Google-Smtp-Source: ABdhPJw2P7A6nXshljTiZVCY6XQHP7hW7W7N6rzA/P88sABrGFIAnvU33l+dpoCxZbX4llaHtBEswg== X-Received: by 2002:a5d:6d06:: with SMTP id e6mr24244598wrq.425.1615226297445; Mon, 08 Mar 2021 09:58:17 -0800 (PST) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id 75sm96993wma.23.2021.03.08.09.58.17 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Mar 2021 09:58:17 -0800 (PST) From: zimoun Date: Mon, 8 Mar 2021 18:57:56 +0100 Message-Id: <20210308175802.62517-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210308175802.62517-1-zimon.toutoune@gmail.com> References: <20210308175802.62517-1-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-dexseq): Move from here... * gnu/packages/bioconductor.scm (r-dexseq): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 --------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f2dd4bb70b..883b6df2fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1525,6 +1525,51 @@ differential expression based on a model using the negative binomial distribution.") (license license:lgpl3+))) +(define-public r-dexseq + (package + (name "r-dexseq") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEXSeq" version)) + (sha256 + (base32 + "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) + (properties `((upstream-name . "DEXSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biomart" ,r-biomart) + ("r-deseq2" ,r-deseq2) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-statmod" ,r-statmod) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DEXSeq") + (synopsis "Inference of differential exon usage in RNA-Seq") + (description + "This package is focused on finding differential exon usage using RNA-seq +exon counts between samples with different experimental designs. It provides +functions that allows the user to make the necessary statistical tests based +on a model that uses the negative binomial distribution to estimate the +variance between biological replicates and generalized linear models for +testing. The package also provides functions for the visualization and +exploration of the results.") + (license license:gpl3+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 64585127e6..4fa4a1e354 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7385,51 +7385,6 @@ includes software to ") (license license:cc0)))) -(define-public r-dexseq - (package - (name "r-dexseq") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DEXSeq" version)) - (sha256 - (base32 - "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) - (properties `((upstream-name . "DEXSeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DEXSeq") - (synopsis "Inference of differential exon usage in RNA-Seq") - (description - "This package is focused on finding differential exon usage using RNA-seq -exon counts between samples with different experimental designs. It provides -functions that allows the user to make the necessary statistical tests based -on a model that uses the negative binomial distribution to estimate the -variance between biological replicates and generalized linear models for -testing. The package also provides functions for the visualization and -exploration of the results.") - (license license:gpl3+))) - (define-public r-annotationforge (package (name "r-annotationforge")