From patchwork Fri May 21 20:26:14 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 29503 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 83F3227BC81; Fri, 21 May 2021 21:34:02 +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 0B55327BC78 for ; Fri, 21 May 2021 21:34:02 +0100 (BST) Received: from localhost ([::1]:48316 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lkBqL-0005IL-8F for patchwork@mira.cbaines.net; Fri, 21 May 2021 16:34:01 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52608) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lkBkn-0005Bp-5n for guix-patches@gnu.org; Fri, 21 May 2021 16:28:17 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:54518) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lkBkm-00032y-Tc for guix-patches@gnu.org; Fri, 21 May 2021 16:28:16 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lkBkm-0000Pe-Pk for guix-patches@gnu.org; Fri, 21 May 2021 16:28:16 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 21 May 2021 20:28:16 +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=B48575.16216288571215 (code B ref 48575); Fri, 21 May 2021 20:28:16 +0000 Received: (at 48575) by debbugs.gnu.org; 21 May 2021 20:27:37 +0000 Received: from localhost ([127.0.0.1]:37775 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBk8-0000JR-Ih for submit@debbugs.gnu.org; Fri, 21 May 2021 16:27:36 -0400 Received: from mail-wm1-f44.google.com ([209.85.128.44]:38828) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lkBjY-0000C5-Of for 48575@debbugs.gnu.org; Fri, 21 May 2021 16:27:07 -0400 Received: by mail-wm1-f44.google.com with SMTP id u4-20020a05600c00c4b02901774b80945cso8061514wmm.3 for <48575@debbugs.gnu.org>; Fri, 21 May 2021 13:27:00 -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=f/xVXtBaE5gloM4h+iHW0NAvupaR04NPZxnb6aSXxEM=; b=IDu/nMkSm0r90gMflyQthrg9kDGN9XYl0g1JTqR+qaanBEFJ2Z5QDZiQTTT5AHzZoJ qQsQsRjILmNyLWpb+j8Qku5OzxEJ31v4zRO1hAAqOAYesAMY+gOjcMMjBUXSzrMIXn2e A73Ft6e/1VN1Q9jaAgvx/jQp8QoXpgB/ZgbdfTd5sg5GG2mRMRKJkusWl6x0lQ9zViDz oK8C35qBlHMC2CAi+4YbAW9tIUAMr9+Hh52CzJmIK2K/ZSB3734rIIE3/bTqKObnpyX4 4KVgKNeHCsZKPmkt+K7ZQvGkAoBCA8HwBrSXvSEMc/3XPo8PhDYu5aPIWM16NUfWCbab FCEQ== 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=f/xVXtBaE5gloM4h+iHW0NAvupaR04NPZxnb6aSXxEM=; b=Zhbd+Xg4un/D/KrqaQ/PB0wSXLpJCs59uTmwz4466IszBGF0cenqQEHQrL8yRo/asi P+B3AVPLxOWQbqW32GVS1G8lx60AmkDfURytWHEXIor0A7OLK1U43VS2L83cqp8r/UZh STUMjz3P64eCUPlEYaJeiZMeOKFWqkThblByyFoFw0yjZt31TxUcZzbpWyHmWPYtOHH4 9sSmpmBSN5zyE4aZJEXrOSifEcvR7xw3DfyjGf5cnp2hyLdr5enri755VzmHj11VdPpA bRZcF4MfFDm1lSWtVxlljEvkAJNuvZ8feKfdlxhFDv6fWAkVBtQVDU6lSHkM36pQsR6x U2Pw== X-Gm-Message-State: AOAM530W0GAlvqGSX/2+aPKefOyFaavo1izpnfSI544pLIT13p5DpiUW /gnHC8Wj2ZJaLsg7bLWPy8UzqyTrUio= X-Google-Smtp-Source: ABdhPJyOTe8u3PBoilELeb9KS0E/KJV/5XpolmfTHAQS9AKPNPr5eKm0iCbkPx7XV9t/ggTvqyyltQ== X-Received: by 2002:a05:600c:410a:: with SMTP id j10mr10586846wmi.5.1621628814268; Fri, 21 May 2021 13:26:54 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id j18sm542711wmq.27.2021.05.21.13.26.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 21 May 2021 13:26:53 -0700 (PDT) From: zimoun Date: Fri, 21 May 2021 22:26:14 +0200 Message-Id: <20210521202622.26591-42-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-mutationalpatterns): Move from here... * gnu/packages/bioconductor.scm (r-mutationalpatterns): ...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 1d38fa1c05..7c471c7375 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3013,6 +3013,51 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) +(define-public r-mutationalpatterns + (package + (name "r-mutationalpatterns") + (version "3.0.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MutationalPatterns" version)) + (sha256 + (base32 + "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) + (build-system r-build-system) + (native-inputs + `(("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ;; These two packages are suggested packages + ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggalluvial" ,r-ggalluvial) + ("r-ggdendro" ,r-ggdendro) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-nmf" ,r-nmf) + ("r-pracma" ,r-pracma) + ("r-purrr" ,r-purrr) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-variantannotation" ,r-variantannotation))) + (home-page "https://bioconductor.org/packages/MutationalPatterns/") + (synopsis "Extract and visualize mutational patterns in genomic data") + (description "This package provides an extensive toolset for the +characterization and visualization of a wide range of mutational patterns +in SNV base substitution data.") + (license license:expat))) + (define-public r-msnbase (package (name "r-msnbase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a1ee4b6772..b5b2cc2f6b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7923,51 +7923,6 @@ secondary structure and comparative analysis in R.") @dfn{RNA-centric annotation system} (RCAS).") (license license:agpl3+))) -(define-public r-mutationalpatterns - (package - (name "r-mutationalpatterns") - (version "3.0.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "MutationalPatterns" version)) - (sha256 - (base32 - "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35")))) - (build-system r-build-system) - (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) - (home-page "https://bioconductor.org/packages/MutationalPatterns/") - (synopsis "Extract and visualize mutational patterns in genomic data") - (description "This package provides an extensive toolset for the -characterization and visualization of a wide range of mutational patterns -in SNV base substitution data.") - (license license:expat))) - (define-public r-chipkernels (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372") (revision "1"))