From patchwork Fri Jan 13 15:07:16 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 46088 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 6E1A027BBEB; Fri, 13 Jan 2023 15:33:36 +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=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 35AA627BBE9 for ; Fri, 13 Jan 2023 15:33:36 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pGLf2-0001ag-JQ; Fri, 13 Jan 2023 10:08:04 -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 1pGLf1-0001aM-8T for guix-patches@gnu.org; Fri, 13 Jan 2023 10:08:03 -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 1pGLf0-0006FG-Vu for guix-patches@gnu.org; Fri, 13 Jan 2023 10:08:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pGLf0-0004zk-7X; Fri, 13 Jan 2023 10:08:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60785] [PATCH] gnu: Add r-maser. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: rekado@elephly.net, guix-patches@gnu.org Resent-Date: Fri, 13 Jan 2023 15:08:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 60785 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 60785@debbugs.gnu.org Cc: rekado@elephly.net X-Debbugs-Original-To: X-Debbugs-Original-Xcc: rekado@elephly.net Received: via spool by submit@debbugs.gnu.org id=B.167362247919190 (code B ref -1); Fri, 13 Jan 2023 15:08:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Jan 2023 15:07:59 +0000 Received: from localhost ([127.0.0.1]:52123 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pGLex-0004zS-D2 for submit@debbugs.gnu.org; Fri, 13 Jan 2023 10:07:59 -0500 Received: from lists.gnu.org ([209.51.188.17]:45358) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pGLes-0004zH-F7 for submit@debbugs.gnu.org; Fri, 13 Jan 2023 10:07:57 -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 1pGLem-0001V3-1w for guix-patches@gnu.org; Fri, 13 Jan 2023 10:07:49 -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 1pGLeg-00068o-Ht for guix-patches@gnu.org; Fri, 13 Jan 2023 10:07:47 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1673622448; x=1675436849; bh=bzGgL+NnM04SAax WbbtygTlWvQo7bxjHnbe6okS4gts=; b=A4KLghHMoBqj4v+iSKBqd5y/oiPtd39 35WhdykpsNRj2bJu91f3n7I2YbinWvuMz55biZAw7GONVeV+9tgy7sV+quy7esa1 yPiJiQkdI3O40O4pOzDksFY3uaQ03wFvsHjIExjMjnpWivBo8d34cKn+F2NbpS0I OiWjO3u+Jzrs= 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 0FAE130021E for ; Fri, 13 Jan 2023 16:07:27 +0100 (CET) Received: from pimi-TRX40-AORUS-PRO-WIFI.lan (77.23.232.54) 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, 13 Jan 2023 16:07:27 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 13 Jan 2023 16:07:16 +0100 Message-ID: <20230113150716.202509-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.38.1 MIME-Version: 1.0 X-Originating-IP: [77.23.232.54] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27382.007 X-TM-AS-Result: No-10--6.441000-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEHwP NZT6pGXGRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v8XjfR3d0weRm1/OiWPM9c7T5D +tWniw5qGsZX0q3FpiOhAZQXEXXZuTvHzGcGqiIKrm7DrUlmNkIAy6p60ZV62fJ5/bZ6npdjKay T/BQTiGrEr7W2UZfO2hm9+SOEShZA00Bl0iQ7ggDvOc5de5pnX53f3bqoWt/s= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.441000-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27382.007 X-TM-SNTS-SMTP: 7970663D955A59597585E1C5730E0FC11C9211A3249D521C44CA9AB84D03A95A2002:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@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/bioconductor.scm (r-maser): New variable. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) base-commit: 789d73234d5b6bbd83bb054146d5bbd1d374d51a diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2fa26cb59..ca236bcf75 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6274,6 +6274,38 @@ (define-public r-makecdfenv package that automatically loads that environment.") (license license:gpl2+))) +(define-public r-maser + (package + (name "r-maser") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "maser" version)) + (sha256 + (base32 + "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv")))) + (properties `((upstream-name . "maser"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-data-table + r-dplyr + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-reshape2 + r-rtracklayer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/DiogoVeiga/maser") + (synopsis "Mapping alternative splicing events to proteins") + (description + "This package provides functionalities for downstream analysis, annotation +and visualizaton of alternative splicing events generated by rMATS.") + (license license:expat))) + (define-public r-metaneighbor (package (name "r-metaneighbor")