From patchwork Fri Apr 8 14:59:54 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 38415 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 E1A7E27BBEA; Fri, 8 Apr 2022 16:01:24 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id AFF0A27BBE9 for ; Fri, 8 Apr 2022 16:01:24 +0100 (BST) Received: from localhost ([::1]:49520 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ncq71-0008WD-Pi for patchwork@mira.cbaines.net; Fri, 08 Apr 2022 11:01:23 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53220) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0008Tf-NZ for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:41662) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ncq6g-0001X3-EU for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ncq6g-0006Xw-Dl for guix-patches@gnu.org; Fri, 08 Apr 2022 11:01:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54790] [PATCH 3/3] gnu: Add r-copykat. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 08 Apr 2022 15:01:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 54790 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54790@debbugs.gnu.org Cc: zimoun Received: via spool by 54790-submit@debbugs.gnu.org id=B54790.164943001325079 (code B ref 54790); Fri, 08 Apr 2022 15:01:02 +0000 Received: (at 54790) by debbugs.gnu.org; 8 Apr 2022 15:00:13 +0000 Received: from localhost ([127.0.0.1]:35557 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5s-0006WL-DM for submit@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:12 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:44910) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncq5q-0006Uj-BP for 54790@debbugs.gnu.org; Fri, 08 Apr 2022 11:00:10 -0400 Received: by mail-wr1-f42.google.com with SMTP id b19so13248659wrh.11 for <54790@debbugs.gnu.org>; Fri, 08 Apr 2022 08:00:10 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=RSVPYpp1ByIX+MOdPLR+WqEBg5BdEHD2ys5Dwm3oOIA=; b=j+hXwvUXMbaWqOMo9lk/3RpKHTxFGBAK6Qgf5aVGuG55YXHtYcj1rPPJnxw3G2CTc9 kzmhaP82A9kUDpt+ycR5K3gIGoaZ4S5bMExQ0TyWHdGnY3uFEngdf3Pe5l0gptz04rs9 is7c/29hD3nduBHVCfwuJX2kIO/aBKgnKyGrUoLUQLVdR8c9T3+aIsJzUdrXDJMxLZL5 UqMuzXTHO8MIKySkL7vR2Vep9EjRNWQtnj+agcQu6B9EXUzqm3MiHSSS3YUzr8XYXZn5 NVYBt/h1BQTJGsVzqbT7cMhEf0k+AR9aNVfeYjvRYfvXgMV1pMTQLKWAhD0wEuHny9eO Be/g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=RSVPYpp1ByIX+MOdPLR+WqEBg5BdEHD2ys5Dwm3oOIA=; b=SDyZg2UeBrb2Aw3VqAjSybZRGDWEpk+uRmL5H6nI7w3yjJZZCprw1ey+/VXGBk8666 iAe+u+b8t838nNu7+RafXbsZ+RK5XfySzKoR2dmrhO2bR3ZMHh35r7TntbSVLZRUHIbE KB66h7tBP0Gq2c9/rD3M2fSXg5k8atDkVKXJyzX+FfB2+LwekxZKT0e4Y1573RJzMRdo LNuq+eG8E4fbQYaBC8T7sPo57MySvM15tU8uRfy5V4cTQ8SNrZE/zi4eMdwMWfZbn2c3 3kT5tlYj7+aCAsuvnDWxZ6e/sUwhZAKe89HxIX8a7o4X0Y+j+xLEFaqdjkGwviVOPO9S UMRg== X-Gm-Message-State: AOAM533BbYUTY7KgK6q5dK8aCYmfV2i+w8QdQdEqlhTOapVulbr7c9Uu 27MQ7xzV+R1L0QiORUS1udDUbW5MCwU= X-Google-Smtp-Source: ABdhPJx5iq4zn1R8NiglR4QyX0bQTdvRTeWZ7Q7d+l8vfiC3g8YsoAZO9Dmo+P3/K7LP5i2wXR1V5Q== X-Received: by 2002:a05:6000:18c3:b0:206:1575:ec8f with SMTP id w3-20020a05600018c300b002061575ec8fmr14565176wrq.479.1649430004653; Fri, 08 Apr 2022 08:00:04 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t185-20020a1c46c2000000b0038e7092025bsm10388554wma.20.2022.04.08.08.00.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 08 Apr 2022 08:00:04 -0700 (PDT) From: zimoun Date: Fri, 8 Apr 2022 16:59:54 +0200 Message-Id: <20220408145954.3345224-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.34.0 In-Reply-To: <20220408145954.3345224-1-zimon.toutoune@gmail.com> References: <20220408145954.3345224-1-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-copykat): New variable. --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 106b25a50b..e3cca9aab8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9138,6 +9138,44 @@ (define-public r-cellchat communication networks from scRNA-seq data.") (license license:gpl3)))) +(define-public r-copykat + (let ((commit ;no tag + "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53") + (revision "0")) + (package + (name "r-copykat") + (version (git-version "1.0.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/navinlabcode/copykat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8")))) + (properties `((upstream-name . "copykat"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-dlm + r-gplots + r-mcmcpack + r-mixtools + r-paralleldist + r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/navinlabcode/copykat") + (synopsis "Inference of genomic copy number from single cell RNAseq data") + (description + "This package Copynumber KAryotyping of Tumors infers genomic copy +number and subclonal structure of human tumors using integrative Bayesian +approaches to identify genome-wide aneuploidy at 5MB resolution in single +cells data. It separates tumor cells and tumor subclones from normal cells +using high-throughput sc-RNAseq data.") + (license license:gpl2)))) + (define-public sambamba (package (name "sambamba")