From patchwork Fri May 21 20:25:50 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29464 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 96BBA27BC81; Fri, 21 May 2021 21:29:09 +0100 (BST) 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_H4, 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 1DA7527BC78 for ; Fri, 21 May 2021 21:29:09 +0100 (BST) Received: from localhost ([::1]:37808 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBlc-0006Bx-Bb for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:29:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52460) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBke-0004Yv-4B for guix-patches@gnu.org; Fri, 21 May 2021 16:28:08 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54495) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkd-0002xe-SI for guix-patches@gnu.org; Fri, 21 May 2021 16:28:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkd-0000Mu-Os for guix-patches@gnu.org; Fri, 21 May 2021 16:28:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:07 +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=B48575.16216288471045 (code B ref 48575); Fri, 21 May 2021 20:28:07 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:27 +0000 Received: from localhost ([127.0.0.1]:37729 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjz-0000Ge-1y for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:27 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:47092) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjN-000095-12 for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:26:49 -0400 Received: by mail-wm1-f48.google.com with SMTP id l18-20020a1c79120000b0290181c444b2d0so1223078wme.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=sJGeC38b9hZlAv1K9htVm4kPdSkSuf9nTVatC5DMh5Y=; b=eCmQDNbK/6cizOeBzPRJblguHN9GpQYSPq0Jsmo/oaRbTMhgNDIeOs8ff5LOxZamaH XrV4nnFYcYhfJp2QDY5P0hGPArAanp1necVVvsPAqP6+mTFbyF9DvZ0o8VlfMpEihN+E xDTJk+cGB/5WJTFQ1giYOzRr1Wt4b6eK6Ie92YrZ1cJctu895CdUhhES5ZGmQbxHXEAZ Q1AVeGsLjW6KlOn6kYY6XXbxNlbg79cG5hGNUbHDL43TnTIh0cHeh3dDlpKS3naxy8c0 yAkdPT1IMvZlISJlDs6tP3u2dQdSuvH2f3FZp5+Lf7TrvSnqgHzHc6emhzmoxXB63YCC uQzw== 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=sJGeC38b9hZlAv1K9htVm4kPdSkSuf9nTVatC5DMh5Y=; b=WEu6HFOEr297niZMWs5zz2cTNzLSQIYSnQpZtcCOMsuSIkt/ykpw5hVKc7ZUYbO+B/ 8j6PSPs1VWYuv4Ad2opOBrifw0zAqNl5h72OTTQv1dk1KoYQHmMdgpMxLm2UijLK72TM /vTf9oxjUc+THuFBJvGEDnnqhiQ2GqQDc8hpgmJVokWNn4J1HB6SuKJUseOy0Zi4VeIE 6jde3t0YlWYmXUrJjYBWNyrDpGTPU8DT4ximdZmDh+1vBhV32KkSOHoWWj0mdaWl9SJH ymhQA7uEdBXyPqWRH8nnKXOI9LlG83X/qFHDonl1M5VAvIbN4KwTQUGUYGhuAxorgd+R vGyA== X-Gm-Message-State: AOAM530DbsARz37cMUvxDZY4V5C51TdcVzwtnXy+at3+QNcEAOY7DT0m XUhGE3unIfUFaf9EmTr/McovrnVBRDs= X-Google-Smtp-Source: ABdhPJz/hYHNnJ8Qj2MzclPsk/N5LkEKeee+/2CKtztewk4xI77wrEkZHnPy3pCkAXOFZtvOs/kHog== X-Received: by 2002:a05:600c:19c8:: with SMTP id u8mr10554960wmq.25.1621628803545; 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.27.2021.05.21.13.26.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:43 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:25:50 +0200 Message-Id: <20210521202622.26591-18-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 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-edaseq): Move from here... * gnu/packages/bioconductor.scm (r-edaseq): ...to here. --- gnu/packages/bioconductor.scm | 40 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 40 --------------------------------- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 69ef513bc6..beb662984d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2127,6 +2127,46 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edaseq + (package + (name "r-edaseq") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EDASeq" version)) + (sha256 + (base32 + "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) + (properties `((upstream-name . "EDASeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-aroma-light" ,r-aroma-light) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsamtools" ,r-rsamtools) + ("r-shortread" ,r-shortread))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/drisso/EDASeq") + (synopsis "Exploratory data analysis and normalization for RNA-Seq") + (description + "This package provides support for numerical and graphical summaries of +RNA-Seq genomic read data. Provided within-lane normalization procedures to +adjust for GC-content effect (or other gene-level effects) on read counts: +loess robust local regression, global-scaling, and full-quantile +normalization. Between-lane normalization procedures to adjust for +distributional differences between lanes (e.g., sequencing depth): +global-scaling and full-quantile normalization.") + (license license:artistic2.0))) + (define-public r-edger (package (name "r-edger") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2edb501f9b..b0de0d9880 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9022,46 +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-edaseq - (package - (name "r-edaseq") - (version "2.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "EDASeq" version)) - (sha256 - (base32 - "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip")))) - (properties `((upstream-name . "EDASeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/drisso/EDASeq") - (synopsis "Exploratory data analysis and normalization for RNA-Seq") - (description - "This package provides support for numerical and graphical summaries of -RNA-Seq genomic read data. Provided within-lane normalization procedures to -adjust for GC-content effect (or other gene-level effects) on read counts: -loess robust local regression, global-scaling, and full-quantile -normalization. Between-lane normalization procedures to adjust for -distributional differences between lanes (e.g., sequencing depth): -global-scaling and full-quantile normalization.") - (license license:artistic2.0))) - (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase")