From patchwork Fri Nov 25 10:03:05 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Navid Afkhami X-Patchwork-Id: 44846 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 BF3DF27BBED; Fri, 25 Nov 2022 10:04:36 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 8C5DF27BBEC for ; Fri, 25 Nov 2022 10:04:35 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oyVZA-0003Nf-3Y; Fri, 25 Nov 2022 05:04:17 -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 1oyVYw-0003N8-DS for guix-patches@gnu.org; Fri, 25 Nov 2022 05:04:05 -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 1oyVYw-00056X-5C for guix-patches@gnu.org; Fri, 25 Nov 2022 05:04:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oyVYw-00048G-06 for guix-patches@gnu.org; Fri, 25 Nov 2022 05:04:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#59567] [PATCH] Added a new package, which is called r-btools. The package is a suite of R function for all types of microbial diversity analyses. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 25 Nov 2022 10:04:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 59567 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 59567@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.166937062415859 (code B ref -1); Fri, 25 Nov 2022 10:04:01 +0000 Received: (at submit) by debbugs.gnu.org; 25 Nov 2022 10:03:44 +0000 Received: from localhost ([127.0.0.1]:33569 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyVYe-00047i-Ft for submit@debbugs.gnu.org; Fri, 25 Nov 2022 05:03:44 -0500 Received: from lists.gnu.org ([209.51.188.17]:45810) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oyVYc-00047Z-8T for submit@debbugs.gnu.org; Fri, 25 Nov 2022 05:03:43 -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 1oyVYY-0003Lr-M0 for guix-patches@gnu.org; Fri, 25 Nov 2022 05:03:40 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oyVYO-0004yC-KP for guix-patches@gnu.org; Fri, 25 Nov 2022 05:03:32 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1669370600; x=1671185001; bh=mxUjy4ayJhHxpsP aMQT0/QllP+N6RcOA8W+NKYGwaMo=; b=B+DV7/LOgyspR7nhtQ+QCnNpnlV/2Wu 2ByxPJmUtBu39erbVwEQakr2kil7esY7oKf4JWVRqqeeNnI7uP0ErJHqtBgDpNOk WdFOQY+QOQyZGciampe8UDufEN6FyHHFiSrZHuX/wqmMUYMAmKkfb88cewXwtoSq r2fPjQBkFKi0= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS id 409573001CD for ; Fri, 25 Nov 2022 11:03:20 +0100 (CET) Received: from localhost.localdomain (89.247.175.75) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.16; Fri, 25 Nov 2022 11:03:17 +0100 From: Navid Afkhami Date: Fri, 25 Nov 2022 11:03:05 +0100 Message-ID: <20221125100305.25836-1-navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 X-Originating-IP: [89.247.175.75] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27284.007 X-TM-AS-Result: No-10--4.667400-5.000000 X-TMASE-MatchedRID: Ebyn40Y01iF6fjezFKxXHE7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOJWs 9XYyBIVFc91aTuTWMRE65t7HvMis8MQeIOzgVmNsULGoTjCGdeUL//VMxXlyE8gVyTd/p+/I4dc Lq1GTrXXdTAmCcpzVLpHUVpTT9o/NRrppn372ENdFdmLrX42PXErYcW9c3HAUU72YOAMDJjieAi CmPx4NwHJnzNw42kCxxEHRux+uk8jfhP1xgyx3DDJXU60gOOQGchICEEs10Ix3ENsx5gGeh/mDx F16jOzM1dCTxTBibdYEaRmO7N2i5FNOongVmZsSpSD4nIcXX6w/0YlpNJ7o8dxSR7be7fnTFTs4 ljtt094P2K/+wkyxVzs7KL+6XFB4pSBl0hpeDh8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.667400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27284.007 X-TM-SNTS-SMTP: 314DBEE31D5AB9D3D43201222CFC37426277934D79876E29EC14A70A9487A1DC2002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-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+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d7097c42c..448d0689a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23,6 +23,7 @@ ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021, 2022 Simon Tournier ;;; Copyright © 2021 Felix Gruber +;;; Copyright © 2022 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; @@ -535,6 +536,41 @@ (define-public pbcopper and utilities for PacBio C++ applications.") (license license:bsd-3)))) +(define-public r-btools + (let ((commit "fa21d4ca01d37ea4d98b45582453f3bf95cbc2b5") + (revision "1")) + (package + (name "r-btools") + (version (git-version "0.0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/twbattaglia/btools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bca593dnxz6xdywpdi0ipli0paln2b3bfxxj0csnmj55ryrz428")))) + (properties `((upstream-name . "btools"))) + (build-system r-build-system) + (propagated-inputs (list r-biomformat + r-coin + r-deseq2 + r-dplyr + r-genefilter + r-phyloseq + r-picante + r-plotly + r-reshape2 + r-stringr + r-vegan)) + (home-page "https://github.com/twbattaglia/btools") + (synopsis "R functiones for microbial diversity analyses") + (description + "An assortment of R functions that ist suitable +for all types of microbial diversity analyses") + (license license:expat)))) + (define-public pbbam (package (name "pbbam")