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Resent-From: Simon Tournier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 17 Jan 2023 17:31:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60885 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60885@debbugs.gnu.org Cc: Simon Tournier Received: via spool by 60885-submit@debbugs.gnu.org id=B60885.16739766599379 (code B ref 60885); Tue, 17 Jan 2023 17:31:01 +0000 Received: (at 60885) by debbugs.gnu.org; 17 Jan 2023 17:30:59 +0000 Received: from localhost ([127.0.0.1]:38130 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnW-0002RB-PP for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:59 -0500 Received: from mail-wm1-f54.google.com ([209.85.128.54]:52101) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnR-0002QT-L5 for 60885@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:54 -0500 Received: by mail-wm1-f54.google.com with SMTP id g10so22858611wmo.1 for <60885@debbugs.gnu.org>; Tue, 17 Jan 2023 09:30:53 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:from:to:cc:subject:date :message-id:reply-to; bh=auZVLsWO+MHZwNV0gcnXtR/xABAK/a8qLlp/YxZVPlc=; b=Am6KVVFNMmFao10jlAwBbDD0yxrezITrURPD9qfFPi5bqnepDWsvp2cVtvAIv8ZYvE pRiFpC3HbI/zNpBszK1WIqlyP+qnb0yZjXnXekA/sI+hxMTkHwO6i4fREDdu93slCHcy /6s6Hrxq7luD1Z80/+OAZ5biZwW8o7K/pNDgsbISUQ+jG5av6F744X3h64wDYgOuSOaw VMKxrbHwCaAhrxcPfmS3S7E6Z9Pc5GeAYpkVCzCO/YRgQDRp/I0L1ufXphd1D2hgLu8s 4HfXLc731ypiEYvJn4yTjj4+p1jgz85sPBlpPUzlqbeQgt/g7A3oouBKbDsXEpghciih u6xQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:references:in-reply-to :message-id:date:subject:cc:to:from:x-gm-message-state:from:to:cc :subject:date:message-id:reply-to; bh=auZVLsWO+MHZwNV0gcnXtR/xABAK/a8qLlp/YxZVPlc=; b=CY4nulqWM6eI2eXyc1lcl+yePS0R8eHkNa+d3CyIfye9Chh5CUDbrjEY6yf50l85PK DZbJz2fnh9HevUOAU44qqnn8pQI/tbxrL7LBZgkk49+gNzx2J7ALJcIyb3AfxRpCHtUH E+KJ73pQsO+ykABjr2+ayCtSbnrRpD8gnpiAi38BqkQBcflA+kjoAuxjyeOo+ee62M0n 64fWQO7e9IkeHfsppRtekKdm55H3qheVFcBdTrtyUjnko3tw4pgFiTo8OoZrGVKQhAJ5 q1iPTzRjT7t9UyZ3HXoL1Ucl5f6Q5PtdQOm6nnUnRMjhHrpgbAtsqPDUPC75LimOCfyI lfQg== X-Gm-Message-State: AFqh2krXL8y6oukSPvqeKanHz5rMwn6vFhAEqIZDF6Z+k8NxcuI1e351 BY6e3ieRKaB4+ZREn7DZHBqQPTd5F6c= X-Google-Smtp-Source: AMrXdXvA5S4wtnPPHZ9jcHiO0MeqH8nnkQGSO/V+z3TTwcjmGCz51M988snisrOFrZ6PK1eheCER1g== X-Received: by 2002:a05:600c:511f:b0:3d2:7ef:acc with SMTP id o31-20020a05600c511f00b003d207ef0accmr1014978wms.0.1673976648017; Tue, 17 Jan 2023 09:30:48 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t12-20020a05600c198c00b003d9de0c39fasm47637107wmq.36.2023.01.17.09.30.47 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 17 Jan 2023 09:30:47 -0800 (PST) From: Simon Tournier Date: Tue, 17 Jan 2023 18:30:39 +0100 Message-Id: <20230117173041.1851206-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 In-Reply-To: <20230117173041.1851206-1-zimon.toutoune@gmail.com> References: <20230117173041.1851206-1-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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-scistreer): New variable. --- gnu/packages/bioconductor.scm | 39 ++++++++++++++++++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca236bcf75..3511bfd81a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2022 Efraim Flashner ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice -;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier +;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka @@ -7343,6 +7343,43 @@ (define-public r-scdblfinder comprehensive scDblFinder method.") (license license:gpl3))) +;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scistreer + (package + (name "r-scistreer") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "scistreer" version)) + (sha256 + (base32 + "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9")))) + (properties `((upstream-name . "scistreer"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-dplyr + r-ggplot2 + r-ggtree + r-igraph + r-paralleldist + r-patchwork + r-phangorn + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-reshape2 + r-rhpcblasctl + r-stringr + r-tidygraph)) + (home-page "https://github.com/kharchenkolab/scistreer") + (synopsis "Maximum-likelihood perfect phylogeny Inference at scale") + (description + "This packages provides fast maximum-likelihood phylogeny inference from +noisy single-cell data using the ScisTree algorithm proposed by +@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}. It makes the +method applicable to massive single-cell datasets (>10,000 cells).") + (license license:gpl3))) + (define-public r-scmap (package (name "r-scmap")