From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id sCU7CLDaxmMRcAAAbAwnHQ (envelope-from ) for ; Tue, 17 Jan 2023 18:28:16 +0100 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id GKQxCLDaxmOEzQAAauVa8A (envelope-from ) for ; Tue, 17 Jan 2023 18:28:16 +0100 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id C09B1B0E5 for ; Tue, 17 Jan 2023 18:28:15 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pHpkj-0002r5-3c; Tue, 17 Jan 2023 12:28:05 -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 1pHpkg-0002qQ-Uz for guix-patches@gnu.org; Tue, 17 Jan 2023 12:28:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pHpkg-0007N0-Mn for guix-patches@gnu.org; Tue, 17 Jan 2023 12:28:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pHpkg-0002Kd-7L for guix-patches@gnu.org; Tue, 17 Jan 2023 12:28:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60885] [PATCH 0/4] Some bioinfo packages Resent-From: Simon Tournier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 17 Jan 2023 17:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 60885 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60885@debbugs.gnu.org Cc: Simon Tournier X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.16739764268892 (code B ref -1); Tue, 17 Jan 2023 17:28:02 +0000 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 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-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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Seal: i=1; s=key1; d=yhetil.org; t=1673976495; a=rsa-sha256; cv=none; b=hJvBMmAqLMsQJwNF5WwTwSAoSlovE6KFA6M37IzsgPSNe9FgGWJdYA7rWMq94RH75RtBAZ mmFkN13xn/VUTBKF1U8ZttgOTPj7c/P0ggTbOi2ewtbvVEd7rckgtcynNO44zAdnEFUKBE Z5fMD6dEUkbHFspnrGgBA1BVlTxvBP2O/TapqdPPnEmdLmhCP4qQDwti0HlcoRHnqUVdjZ 7bkgdlsK1pAdFOjJ+vJU65PpQKA27cx4sQ7/4idN5rcQ0lwe6JzzaUhqGy3ETysw49ubbW ssatDvjWaCaLvNoOQ1v74OojmgvB8Y577Id5s/LI2A1k2YNlgKxnKUpY0fWtzQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=ExAQtf+f; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1673976495; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=qZxOxQ15jxxZU/t9V9QOzwVwmio5rGcszUqzMw5LmYI=; b=EpOpNmqUvtz3WeVi3+KiHbHQWShCU3T05PwWEWFxhwF9TzDhYxlSe7Kt89tbtbeAATQGrb s/qJcHwLKLkDEpsJQ/sgK5IkDsT4Y9AZpL+jOwKBRRvKvMsKtDogUVF8xWdJ8OutW8ItER keuLwdt+BOA2eMg225JDuG7UwmK1XHX6Ncwa8l2RbWkacjPXxPfgUeNwxGDJaH1BgDVJ0R ccqh3MsX5NOm3QCvq0ZyvD61sQBx4K7w1QPeUitPHHtph+Dbz2OgM7WCNZsX3RuXLSTdMH JG+B7Hu3oYXckj8wglihiMta2B6GDJ/3/ug6x4c1TxUI/KoGFj2lmzyv6uWzzw== X-Migadu-Scanner: scn0.migadu.com X-Migadu-Spam-Score: -2.73 X-Spam-Score: -2.73 X-Migadu-Queue-Id: C09B1B0E5 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=ExAQtf+f; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-TUID: adTDdoW3HYrD 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