From unknown Thu Aug 21 12:10:03 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#60885 <60885@debbugs.gnu.org> To: bug#60885 <60885@debbugs.gnu.org> Subject: Status: [PATCH 0/4] Some bioinfo packages Reply-To: bug#60885 <60885@debbugs.gnu.org> Date: Thu, 21 Aug 2025 19:10:03 +0000 retitle 60885 [PATCH 0/4] Some bioinfo packages reassign 60885 guix-patches submitter 60885 Simon Tournier severity 60885 normal tag 60885 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 17 12:27:06 2023 Received: (at submit) by debbugs.gnu.org; 17 Jan 2023 17:27:06 +0000 Received: from localhost ([127.0.0.1]:38120 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpjl-0002JL-Md for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:27:06 -0500 Received: from lists.gnu.org ([209.51.188.17]:45272) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpjh-0002Iu-Iv for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:27:04 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pHpjh-0002m1-DN for guix-patches@gnu.org; Tue, 17 Jan 2023 12:27:01 -0500 Received: from mail-wr1-x42f.google.com ([2a00:1450:4864:20::42f]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pHpjf-0007IB-Jd for guix-patches@gnu.org; Tue, 17 Jan 2023 12:27:01 -0500 Received: by mail-wr1-x42f.google.com with SMTP id e3so22144838wru.13 for ; Tue, 17 Jan 2023 09:26:58 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=qZxOxQ15jxxZU/t9V9QOzwVwmio5rGcszUqzMw5LmYI=; b=ExAQtf+fpZPQUaZ2jLShITnwZ3/+46Y/4vBbLz80taRI0/8wzHYxkk024tWrSbGupP j9cdipc40m30ayUvB5vV7oH8EfCRAbtlNGej3nmSyDcQQH07BlZ45GnypRNuRBHjK/Sl 8Q7qWAOPae6XWZwhR4oUXFCDHBf7ssmCz0WpSANWPlZiU14bsDsveqfT6XO7vHSS5CrM dwJc91BC7jbgBRHrYmmM9is9yjxyEWCB8pi9K+DOjgLVK5YH1ZgWq1/hx2AJ4N7hwSip f9T56zMrkShlzENjuXMHifDnvHnaTHvPkVrl/EntRaf5sensu0qR9gr+ELsDP+UVUq+V augg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=qZxOxQ15jxxZU/t9V9QOzwVwmio5rGcszUqzMw5LmYI=; b=Cxu/JjGJG8YRdmYDULRykkWBkXXttDB5006NkyfMLP3e1TboornLfFDPij3lqpyKI4 h+WVG/3BgjF7rse8fq/rvrO/8gbC7Od/8dE/qj3OyYYI15aqsGECxD951QU/RQAfJLT0 TxzoqsDdGc4rVuHt+y7E57E0OVJB3NOGITCnPGrkUCiPSbysn1bAiqjTFg/x/U4IYp3t yOyPQkiTC9qrl5KMsxMjZEz4pfQpi7vtu1FR6PJAr1lRlO+5kRvNftrjhB6efH/GxnnI +AgO95fc+VeQ5a8zWFmyZwdxBsz+94HT86OE/gnnDnonmIRnm9zUoU8V4YLtsYXiyW3L htdQ== X-Gm-Message-State: AFqh2koweVH5yj6x7GjRBVxhwM4N2fRAM6VUEFbai20Fk87B42JELo4J hfAIUEqUTmtTOl/VUwn18XrUTYS3xTA= X-Google-Smtp-Source: AMrXdXuVsDNAHNBr1lRyN9jShAkQICwY8nMA4CEtdGElqaKqiLZ3dD/4cV3BszWvIZ/uo9GQvy3tcw== X-Received: by 2002:a5d:6b0e:0:b0:2be:1672:748b with SMTP id v14-20020a5d6b0e000000b002be1672748bmr681742wrw.0.1673976417736; Tue, 17 Jan 2023 09:26:57 -0800 (PST) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id p8-20020a5d4588000000b002bdfb97e029sm7274052wrq.19.2023.01.17.09.26.57 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 17 Jan 2023 09:26:57 -0800 (PST) From: Simon Tournier To: guix-patches@gnu.org Subject: [PATCH 0/4] Some bioinfo packages Date: Tue, 17 Jan 2023 18:26:50 +0100 Message-Id: <20230117172650.1849207-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::42f; envelope-from=zimon.toutoune@gmail.com; helo=mail-wr1-x42f.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -2.3 (--) Hi, Here some pacakages used in Bioinformatics. Note that the package numbat comes with 'bin/pileup_and_phase.R' for preparing the data, as explained in online documentation [1]. Here, this script goes under 'site-library/numbat/bin' which does not perfectly match the online documentation mentioning 'numbat/inst/bin/' instead. 1: https://kharchenkolab.github.io/numbat/articles/numbat.html Cheers, simon Simon Tournier (4): gnu: Add python-vireosnp. gnu: Add r-scistreer. gnu: Add r-roptim. gnu: Add r-numbat. gnu/packages/bioconductor.scm | 106 +++++++++++++++++++++++++++++++- gnu/packages/bioinformatics.scm | 22 +++++++ gnu/packages/cran.scm | 23 ++++++- 3 files changed, 149 insertions(+), 2 deletions(-) base-commit: ecda67a577570f412b103e5dd8ed1a44193a9c11 -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 17 12:30:55 2023 Received: (at 60885) by debbugs.gnu.org; 17 Jan 2023 17:30:55 +0000 Received: from localhost ([127.0.0.1]:38128 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnT-0002Qu-DE for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:55 -0500 Received: from mail-wm1-f50.google.com ([209.85.128.50]:53221) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnR-0002QS-IX for 60885@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:53 -0500 Received: by mail-wm1-f50.google.com with SMTP id k16so2222210wms.2 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:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=lVLm3ddftblMTbpRAtwmVsQp3PzpYgcJYRPggL1e4Zc=; b=qt+X9Z+67CM/1qEhD97ciG6wsYzWrJTVje+J8rNMSdVUAuB2X+qSU6UNhTOd8b1BsL 092FPgjNVQC1fqrVmcF9Mx/i92l8VDkT7W4vr0oj+nZCuX2iIs+6sLcuO1sFJN5Wd2TS bMv2vlYrVIPmZq2xeaxrVIkNgmeaVk2dxk1rgWdheNdkDtgxCz8vbiNj92lTBpZzfUb5 /RWd3Nwh4Ty0Wr3TtsZ30AXPYmnyp4sc1wsSlACnzVIwh8iFJMAcD+n8Rbjn/ND3dla5 KI74t+16CSZci9SGHPgGz1DGkQ/SWtMbtnNVr5FNPREDhPs5TntNa9gOMQRI4DTNO4sh sgtg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=lVLm3ddftblMTbpRAtwmVsQp3PzpYgcJYRPggL1e4Zc=; b=INXn3Pr3X0NZD1BUVcjNal5gLO5yJQvRClzYOv+ctxMNzTeNcMXmu5a5bONZ0E9p0v 4qKqxnbP5aoS09qpIeiONIr3kB1oR2vEYHzwfyj+lFiRc4VHJxgRRfkkVNgn2Sl5sl0E 8EQwvjqLWtq4ocfLfNkN7sWkRNYIqWsiTsePA4zLXFwwIHLaSAOpV24zSpqE1WV2Hnvs R+AP97Kvc/A4bTBRAmNDj10FLQBg1UibUEAK2KC6Nk4N1gjIaMX6O4YVQQgdOmYDLlSx vStp1JvddEMQWM1jjL33G5RDXjVUgpurRrm5XtegsXRZ4dYL6AVsIhzNO+uS8TzGyN0Y n3Gw== X-Gm-Message-State: AFqh2kpTrXXtHTmzEBA5fV4jC9Nr5p7dg1o+OZ+IVrO+eKNetd/52mxA I2ElIaLtg7Yb76oZMR488iD9IDDnQKs= X-Google-Smtp-Source: AMrXdXupNulyP7MHnAtILB5Zd8LdsoI3/BAc/DhAbr6WHDQ3egxwdOeKpRlBHDiALftY5Dn1Kb26rQ== X-Received: by 2002:a7b:c849:0:b0:3db:303:2724 with SMTP id c9-20020a7bc849000000b003db03032724mr983060wml.1.1673976647595; Tue, 17 Jan 2023 09:30:47 -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 To: 60885@debbugs.gnu.org Subject: [PATCH 1/4] gnu: Add python-vireosnp. Date: Tue, 17 Jan 2023 18:30:38 +0100 Message-Id: <20230117173041.1851206-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60885 Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioinformatics.scm (python-vireosnp): New variable. --- gnu/packages/bioinformatics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e60dffc21e..5fc2d18690 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17604,6 +17604,28 @@ (define-public r-kbet ;; Any version of the GPL (license license:gpl3+)))) +(define-public python-vireosnp + (package + (name "python-vireosnp") + (version "0.5.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "vireoSNP" version)) + (sha256 + (base32 + "02ybhzivsxwnb1axlgbs63wni1j27xajnkl4jw1ps5vmsz2l4b0d")))) + (build-system python-build-system) + (propagated-inputs (list python-matplotlib python-numpy python-scipy)) + (home-page "https://github.com/huangyh09/vireoSNP") + (synopsis "Deconvolution based on SNP for multiplexed scRNA-seq data") + (description + "This package provides a deconvolution based on Single Nucleotide +Position (SNP) for multiplexed scRNA-seq data. The name vireo stand for +Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in +multiplexed scRNA-seq data and follows the clone identification from +single-cell data named @url{https://github.com/PMBio/cardelino, cardelino}.") + (license license:asl2.0))) + (define-public ccwl (package (name "ccwl") -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 17 12:30:59 2023 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 To: 60885@debbugs.gnu.org Subject: [PATCH 2/4] gnu: Add r-scistreer. 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 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60885 Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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") -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 17 12:30:59 2023 Received: (at 60885) by debbugs.gnu.org; 17 Jan 2023 17:30:59 +0000 Received: from localhost ([127.0.0.1]:38132 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnX-0002RE-6i for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:59 -0500 Received: from mail-wm1-f46.google.com ([209.85.128.46]:55158) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnS-0002QW-Qt for 60885@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:55 -0500 Received: by mail-wm1-f46.google.com with SMTP id m15so1669866wms.4 for <60885@debbugs.gnu.org>; Tue, 17 Jan 2023 09:30:54 -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=/X+/LHDa7Yb9jGbbBOa4e67Jq5mj9Rtl/wS0sIduITM=; b=MqxIvnfSV7ifs5RWvfWZxeSdfgRwlE2AXnEJPNrLImLe1xg8xwHh0xCiVupGQl4zUh rIO9U/ACV+elY3uTUaOjSUtIYdDR1a08xrKlJMQPzwI1sRvAIZaoEqwqZ0ydfiRBUaMy F5Y+JTaV3oxTA7HqIsjjZym6ehiv8W5hq9H0hqq3aHOkIu8nPMQud4OB1OOelXtx5J7k 6JkrJ2X9BJBKJ4X6i3t1b1InAVP9NNs8bpEpOX4Q4j/ihW/0oVVeGi7dYAlo+sXxs7Di Iud3uXaWVY7g4U97r+gDT8R86jsOFieewhPdaQfRRLIGCymYzOi1nJuCP77blV86DAxM rwug== 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=/X+/LHDa7Yb9jGbbBOa4e67Jq5mj9Rtl/wS0sIduITM=; b=EscBRxiKDldx/FhneQpjZsAdzFHMUwiuCnpRwbKW7NzYpT66RqZAw4kFNnRIgtSoau bL3fw0fZ9ABbXmlEhCZSRP3zgl2stquHCecq3gPM/xA4UDo/b+I4V0SN3s7JtJRs/kzM RJ262TZPvINTN4MDgtehWSkK7ODwv+YGnXQOOKOdJ3+LXzz6XevmSmvIeKuuIHO0qiJb dQL6wbgAXuZGRW4D3NGKg2aaCdJNi4zUGTLum3u/y5DMiPzFw2dKerUaq4RrL+fu/bTO PFccNe2RJ7wuuzYJhBZpobZolv94IKjJa3wEJPWf6AeCOBZJwu1HPhxYSoh/oZ/ZZjUQ hBSw== X-Gm-Message-State: AFqh2krqQKgIVdjWsawCNV9DqI3uHQ2KG10NobzSqNTWWdVkVo2Grdvg Xwl1lhvpoAy5DGY0HKEx+s7ArY8pY6M= X-Google-Smtp-Source: AMrXdXvz5/ZeGdruWZutzHAMh1Pch9TtssID0V+ZKURAHLAB7gnDbcosmdDchMhvnMWJgTRaY4kgUg== X-Received: by 2002:a05:600c:3b05:b0:3d3:4f99:bb14 with SMTP id m5-20020a05600c3b0500b003d34f99bb14mr923791wms.0.1673976648947; 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.36.2023.01.17.09.30.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 17 Jan 2023 09:30:48 -0800 (PST) From: Simon Tournier To: 60885@debbugs.gnu.org Subject: [PATCH 4/4] gnu: Add r-numbat. Date: Tue, 17 Jan 2023 18:30:41 +0100 Message-Id: <20230117173041.1851206-4-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 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60885 Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioconductor.scm (r-numbat): New variable. --- gnu/packages/bioconductor.scm | 67 +++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3511bfd81a..2d6093b238 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6696,6 +6696,73 @@ (define-public r-mzr previously been used in XCMS.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-numbat + (package + (name "r-numbat") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "numbat" version)) + (sha256 + (base32 + "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + (properties `((upstream-name . "numbat"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-catools + r-data-table + r-dendextend + r-dplyr + r-genomicranges + r-ggplot2 + r-ggraph + r-ggtree + r-glue + r-igraph + r-iranges + r-logger + r-magrittr + r-matrix + r-optparse + r-paralleldist + r-patchwork + r-pryr + r-purrr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-roptim + r-scales + r-scistreer + r-stringr + r-tibble + r-tidygraph + r-tidyr + r-vcfr + r-zoo)) + (home-page "https://github.com/kharchenkolab/numbat") + (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") + (description + "This package provides a computational method that infers copy number +variations (CNV) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. It integrates signals from gene expression, allelic ratio, and +population haplotype structures to accurately infer allele-specific CNVs in +single cells and reconstruct their lineage relationship. It does not require +tumor/normal-paired DNA or genotype data, but operates solely on the donor +scRNA-data data (for example, 10x Cell Ranger output). It can be used to: + +@enumerate +@item detect allele-specific copy number variations from single-cells +@item differentiate tumor versus normal cells in the tumor microenvironment +@item infer the clonal architecture and evolutionary history of profiled tumors +@end enumerate + +For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, +Gao et al in Nature Biotechnology 2022}.") + (license license:expat))) + (define-public r-organism-dplyr (package (name "r-organism-dplyr") -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jan 17 12:30:59 2023 Received: (at 60885) by debbugs.gnu.org; 17 Jan 2023 17:31:00 +0000 Received: from localhost ([127.0.0.1]:38134 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnX-0002RL-JP for submit@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:59 -0500 Received: from mail-wm1-f48.google.com ([209.85.128.48]:51114) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pHpnS-0002QU-4X for 60885@debbugs.gnu.org; Tue, 17 Jan 2023 12:30:56 -0500 Received: by mail-wm1-f48.google.com with SMTP id j17so4333478wms.0 for <60885@debbugs.gnu.org>; Tue, 17 Jan 2023 09:30:54 -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=EWVVlBqMsPVKZsWIuTicE0JKaQwL5FZOsIQXfNJrIXg=; b=nUWJvzF/qgpmSFSsCWA0fnRzNIEojfzpU1l1HWn+3xbkCyp0is2n07Br3vgBPjAdJZ 04QMJZErG6qFsj8oBAhGZ4qE6frSRAIT/+9HVgvhVJgD1w+78PXxL2h5yETPi89HipBJ 592pMQ9PE6dJRFzZLGxxskWRZY1X7tatrJuhWc67FsqHgWo24TvXmVhDLxBs1jHwgvoA ArD5CxcmDNFFFf+1Uw/Z1usrh5Cm1/fIEzP9T9m4UjwKjOBzdyJD2FdoqikDlRUQq+Ze sy4ZMlZ+5haR4RL+WBWex74f7Xcieq0eLUMuqwKm+H9ldms4L1EEce/ZjrFbPI2lBNEe nMfA== 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=EWVVlBqMsPVKZsWIuTicE0JKaQwL5FZOsIQXfNJrIXg=; b=o7wvDVk3Dr1sRDD+DN+5kl6B5fnLoiecQDiMNNwoDn8c8Z3o8OU27XI0/AumtBAQpd fveJKjmfg0KX0j154HXz0EB+yJuf+G2jmpl2CpFTymjXXKTvoxHxli8gQG8fPHA6jnjz bkoBd+72i4HEyVxeHa/hYk5g+zf84DT8mQgIudBz6p4Nx6V+SEiYTJW3Hi78v2C6JM0q 521adah7mjBUYBqHPD3TY2Pkd5v/dnh09CWDTzzNJ0ckgRGOPPUY0ZAKoEllpKT0MaCB lRtdF16ZAmjDdYodQ/EkysEhhQEMszxcWQ7iT+srBHgP1zezmWif8WxpiCizz1kxSVe4 FFKw== X-Gm-Message-State: AFqh2krIrHkqEY0TqG/flfemJVrVTMbtTAf7nakh9XfZ+Zo91UQb24wM m/PmPsFW0DoP3BLjNtaZNeV0uj+p0tE= X-Google-Smtp-Source: AMrXdXsBmdphX3MWiSugxm/buPxBt1cpHtzYfO1QdD9cWegK7T2vhJqdFPbKaQsiKaZArtFR8ipU1A== X-Received: by 2002:a05:600c:3b29:b0:3da:f7a9:50ca with SMTP id m41-20020a05600c3b2900b003daf7a950camr991878wms.0.1673976648518; 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.36.2023.01.17.09.30.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 17 Jan 2023 09:30:48 -0800 (PST) From: Simon Tournier To: 60885@debbugs.gnu.org Subject: [PATCH 3/4] gnu: Add r-roptim. Date: Tue, 17 Jan 2023 18:30:40 +0100 Message-Id: <20230117173041.1851206-3-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 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60885 Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/cran.scm (r-roptim): New variable. --- gnu/packages/cran.scm | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3fcbd3b9f6..aad49b4524 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -31,7 +31,7 @@ ;;; Copyright © 2020 Antoine Côté ;;; Copyright © 2020 Arun Isaac ;;; Copyright © 2020 Magali Lemes -;;; Copyright © 2020, 2021, 2022 Simon Tournier +;;; Copyright © 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Aniket Patil ;;; Copyright © 2021 Marcel Schilling ;;; Copyright © 2021 Guillaume Le Vaillant @@ -9214,6 +9214,27 @@ (define-public r-randomizr experimental designs and random samples for common sampling designs.") (license license:expat))) +(define-public r-roptim + (package + (name "r-roptim") + (version "0.1.6") + (source (origin + (method url-fetch) + (uri (cran-uri "roptim" version)) + (sha256 + (base32 + "11h6qdi0rsv0bpps6nxkzzapan284q0gldzkmgx3ww5kvnic5w3y")))) + (properties `((upstream-name . "roptim"))) + (build-system r-build-system) + (propagated-inputs (list r-rcpp r-rcpparmadillo)) + (home-page "https://github.com/ypan1988/roptim/") + (synopsis "General purpose optimization in R using C++") + (description + "This package performs optimization in R using C++. A unified wrapper +interface is provided to call C functions of the five optimization algorithms +('Nelder-Mead', BFGS', CG', L-BFGS-B and SANN') underlying @code{optim()}.") + (license license:gpl2+))) + (define-public r-base64url (package (name "r-base64url") -- 2.38.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 20 04:57:41 2023 Received: (at 60885-done) by debbugs.gnu.org; 20 Jan 2023 09:57:41 +0000 Received: from localhost ([127.0.0.1]:45628 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pIo9V-0000PF-09 for submit@debbugs.gnu.org; Fri, 20 Jan 2023 04:57:41 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21109) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pIo9P-0000P3-O8 for 60885-done@debbugs.gnu.org; Fri, 20 Jan 2023 04:57:39 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1674208652; cv=none; d=zohomail.com; s=zohoarc; b=XV1B9C50Z3z9Jyc6WB4PybbFtQaMATn4vHzC4qKUFTMmeftpRaooE78u/vWL5Kt/m3fF4ObMCBQNFIgHrrNczToxUe44tLAMUAKX/zqgv5ebzo16enze7DWHiG59uYXwbBZj8+kfOJ3jdHUIR6QO9zSMRa9mejbUFf2ZZKn1qRM= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1674208652; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=D8o8Ubt5AMAqaR7m5Ekl6CbpSejMDCAXP6VYSK2eIk4=; b=RRHKmwdGw0sk0FqBlHDIAT9C0Ox42xk5pjEdgXkPCBZA69s1kdt7R/vV3UioGJdG2sjB9nQf+uzSU/92t2ipbmzyaaApmqxqMeU+3zr6zgkaMI5qyo6WVoQ22juhCljh5vAwIRdqMQkN/HF/tVr6TV0m2/KUKJoHTlLVnvI4EFM= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1674208652; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=D8o8Ubt5AMAqaR7m5Ekl6CbpSejMDCAXP6VYSK2eIk4=; b=Yfe7kcxHcx7TRp3lXKxi2IiaIhwgiEKKXlrFpNbD4Ryzh0QDW2O+X9i6ywKBOVZ4 GrJQZ1jtTECdDcfY2LxRx8b36m8Ee3Hij+aMOMkjDmFfspBBWek5Fhx4rIkWJNS3Ayu fK2hMjdSDGz7VZQuVXvjSb3golyMZ0JsMXBps42Y= Received: from localhost (196-108-142-46.pool.kielnet.net [46.142.108.196]) by mx.zohomail.com with SMTPS id 1674208651374712.1827826656687; Fri, 20 Jan 2023 01:57:31 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 60885-done@debbugs.gnu.org Subject: [PATCH 0/4] Some bioinfo packages Date: Fri, 20 Jan 2023 10:56:54 +0100 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87zgadh6k7.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60885-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thank you for the patches! I applied them with very minor changes to descriptions. -- Ricardo From unknown Thu Aug 21 12:10:03 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 17 Feb 2023 12:24:10 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator