From patchwork Fri Mar 5 01:20:39 2021 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: 27446 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 A0FBB27BC50; Fri, 5 Mar 2021 01:22:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id DFB7E27BC4F for ; Fri, 5 Mar 2021 01:22:15 +0000 (GMT) Received: from localhost ([::1]:52070 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lHzAV-0004K0-4d for patchwork@mira.cbaines.net; Thu, 04 Mar 2021 20:22:15 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:38050) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lHzAJ-0004HT-Nl for guix-patches@gnu.org; Thu, 04 Mar 2021 20:22:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:49127) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lHzAJ-000866-Cx for guix-patches@gnu.org; Thu, 04 Mar 2021 20:22:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lHzAJ-0005f3-9W for guix-patches@gnu.org; Thu, 04 Mar 2021 20:22:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#46937] [PATCH 3/3] gnu: Add r-circrnaprofiler. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 05 Mar 2021 01:22:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46937 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46937@debbugs.gnu.org> Cc: rekado@elephly.net, =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmE=?= =?utf-8?b?yJljdQ==?= Received: via spool by 46937-submit@debbugs.gnu.org id=B46937.161490727421688 (code B ref 46937); Fri, 05 Mar 2021 01:22:03 +0000 Received: (at 46937) by debbugs.gnu.org; 5 Mar 2021 01:21:14 +0000 Received: from localhost ([127.0.0.1]:60671 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9V-0005dk-Kj for submit@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:13 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:60835) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lHz9T-0005dK-MY for 46937@debbugs.gnu.org; Thu, 04 Mar 2021 20:21:12 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id CB7DE3000DE; Fri, 5 Mar 2021 02:21:05 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1614907265; x=1616721666; bh=If8Ji49LgH5sbIR7EXedEs3PUFtJ+vAGxQB KorBTh4I=; b=NVrc/J9IJ3qPLaPRt0qiXl5dscm9UsyDoTAF7w0oIJv685qYuyW cXeNV+Xa1i++p/MHtPzWgmHw1PW1KFLvZZpXRodjs6x14cShYhO1+19cOZ6zshPJ EQfMUhhL33+NjI/TLdnSkA2aglv4KJQwwOp1tyzwBVIpOeG84gD8sFlI= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id VISoKwoyooWp; Fri, 5 Mar 2021 02:21:05 +0100 (CET) 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; Fri, 5 Mar 2021 02:21:05 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2176.2; Fri, 5 Mar 2021 02:21:04 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Fri, 5 Mar 2021 02:20:39 +0100 Message-ID: <20210305012039.15219-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> References: <20210305012039.15219-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-AS-Result: No-10--3.693300-8.000000 X-TMASE-MatchedRID: qYH9YzLp+XssaaYlMvaOHAPZZctd3P4BlwT0XposETUIP8WG05jq8Abo TDS3zulAkzpHopPQfRr9E3D6X+2jHW2x/ChgpGE+TT9ZveSPAxX4qCLIu0mtIPj/xqm3b+MoP4x DpnkWHW8c3dYpQhN0IYHDDaAVX9kI8T3ZGQTX60nRSfdpjZZR7lF5adRR2Ej1tSlhqC3qPOh2Pq BW66jvyVbRH5B/+lqLUw3F1+6WUPyhznSgFQVXH6ubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIab3/xwmHh63msfUuHRu7UH8o0m4F7lG1Jq7PhR+u3KVM0bb4LD/gftvfRVd2xp0GrUok9 zSnsZir26sKykYIkfL0ZBgLRyUHz+Bepavj7kpF4W/rV0NGdh/RzmpSOCosq9iVB5TfGsfRe0Ym bY3/fIg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.693300-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.004 X-TM-SNTS-SMTP: 8B6D5D5A91A402B4F6FDFBD7C01B739A2BECB42538212C7EA11445D4338671F62000:F 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" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable. --- gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55a9b07509..2da2be6ae3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6810,6 +6810,59 @@ accessibility data.") ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) +(define-public r-circrnaprofiler + (package + (name "r-circrnaprofiler") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "circRNAprofiler" version)) + (sha256 + (base32 + "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn")))) + (properties + `((upstream-name . "circRNAprofiler"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) + ("r-deseq2" ,r-deseq2) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-gwascat" ,r-gwascat) + ("r-iranges" ,r-iranges) + ("r-magrittr" ,r-magrittr) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-reshape2" ,r-reshape2) + ("r-rlang" ,r-rlang) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-seqinr" ,r-seqinr) + ("r-stringi" ,r-stringi) + ("r-stringr" ,r-stringr) + ("r-universalmotif" ,r-universalmotif))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://github.com/Aufiero/circRNAprofiler") + (synopsis + "Computational framework for the downstream analysis of circular RNA's") + (description + "@code{r-circrnaprofiler} is a computational framework for a comprehensive +in silico analysis of @dfn{circular RNA} (circRNAs). This computational +framework allows to combine and analyze circRNAs previously detected by +multiple publicly available annotation-based circRNA detection tools. It +covers different aspects of circRNAs analysis from differential expression +analysis, evolutionary conservation, biogenesis to functional analysis.") + (license license:gpl3))) + (define-public r-cistopic (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") (revision "0"))