From debbugs-submit-bounces@debbugs.gnu.org Mon Jun 27 18:18:32 2022 Received: (at submit) by debbugs.gnu.org; 27 Jun 2022 22:18:32 +0000 Received: from localhost ([127.0.0.1]:53545 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o5x3w-00048y-8e for submit@debbugs.gnu.org; Mon, 27 Jun 2022 18:18:32 -0400 Received: from lists.gnu.org ([209.51.188.17]:43156) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o5x3s-00048o-Ij for submit@debbugs.gnu.org; Mon, 27 Jun 2022 18:18:30 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:42058) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o5x3s-0006zN-BY for guix-patches@gnu.org; Mon, 27 Jun 2022 18:18:28 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:43595) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o5x3p-0004Zv-16 for guix-patches@gnu.org; Mon, 27 Jun 2022 18:18:27 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 6680116025C for ; Tue, 28 Jun 2022 00:18:21 +0200 (CEST) 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:received:received; s=mdc; t=1656368300; x=1658182701; bh=yWo6fIVQYMhuBeDTfO0Bu3DQXekG/HkQSRSzuOUba98=; b=YvJkqUvuk9Qw nPMYVYwdane1T0WozKRgF/SwRboUScMatGBfnlyaDs/VXZGtgNp2hUWVGpxXIVz+ vUDqP2B5I3BsQVogH/sxcNSCCQ8aUAMP8nH80M/tFKsWt7Ov+kEQXSRVMXHrLIqK hpkZOEZ+5himniGod6QfD8rxLkO6mQo= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id XvzwXIWo7Qom for ; Tue, 28 Jun 2022 00:18:20 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Tue, 28 Jun 2022 00:18:20 +0200 (CEST) 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 15.1.2507.9; Tue, 28 Jun 2022 00:18:19 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: Add r-bambu. Date: Tue, 28 Jun 2022 00:17:52 +0200 Message-ID: <20220627221752.20017-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-26982.003 X-TM-AS-Result: No-10--7.542400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJMnA6yEJMgMSgrcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt8Z8zsjIitoJnVTWWiNp+v9ZDdHiTk9OcKY5ZGw7wyeHycO hvTXTlouSkIUZyUQUJ1365UWdO2/F0N7DjAdxZNTi8zVgXoAltjX6XtdE9yLDC24oEZ6SpSl2+n EixMccdpFOlJCK/1ftTg/F8SJNhCsX9WkiB8KjvxvD2NLHoTq6RAIP3DuirdgzWLnK9qd/g9HCm G4Mns+Y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.542400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26982.003 X-TM-SNTS-SMTP: 566A03F5343914F13FF05C89FBE114452CFA0AE4B642A99D0758A0706A1B15472002:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=b2062.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, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit 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: -2.4 (--) * gnu/packages/bioconductor.scm (r-bambu): New variable. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..7d8df496eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2029,6 +2029,49 @@ (define-public r-aneufinder sequencing data.") (license license:artistic2.0))) +(define-public r-bambu + (package + (name "r-bambu") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bambu" version)) + (sha256 + (base32 + "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w")))) + (properties `((upstream-name . "bambu"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-bsgenome + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tidyr + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/GoekeLab/bambu") + (synopsis + "Isoform reconstruction and quantification for long read RNA-Seq data") + (description + "This @code{R} package is for multi-sample transcript discovery and +quantification using long read RNA-Seq data. You can use @code{bambu} after +read alignment to obtain expression estimates for known and novel transcripts +and genes. The output from @code{bambu} can directly be used for visualisation +and downstream analysis, such as differential gene expression or transcript +usage.") + (license license:gpl3))) + (define-public r-biocversion (package (name "r-biocversion") base-commit: 144a750f8b10e606751bc887bcb09e7fb7ae09ff -- 2.36.1