From patchwork Thu Aug 18 11:09:42 2016 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 14746 Received: (qmail 26377 invoked by uid 89); 18 Aug 2016 11:11:29 -0000 Authentication-Results: sourceware.org; auth=none X-Virus-Checked: by ClamAV 0.99.2 on sourceware.org X-Virus-Found: No X-Spam-SWARE-Status: No, score=-2.5 required=5.0 tests=AWL, BAYES_00, RP_MATCHES_RCVD, SPF_PASS autolearn=ham version=3.3.2 spammy=wish X-Spam-Status: No, score=-2.5 required=5.0 tests=AWL, BAYES_00, RP_MATCHES_RCVD, SPF_PASS autolearn=ham version=3.3.2 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on sourceware.org X-Spam-Level: X-HELO: lists.gnu.org Received: from lists.gnu.org (HELO lists.gnu.org) (208.118.235.17) by sourceware.org (qpsmtpd/0.93/v0.84-503-g423c35a) with ESMTP; Thu, 18 Aug 2016 11:11:18 +0000 Received: from localhost ([::1]:51918 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1baLED-00049W-B4 for patchwork@sourceware.org; Thu, 18 Aug 2016 07:11:17 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:41587) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1baLE8-00049Q-HR for guix-devel@gnu.org; Thu, 18 Aug 2016 07:11:13 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1baLE5-0002fN-9v for guix-devel@gnu.org; Thu, 18 Aug 2016 07:11:12 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:56737) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1baLE5-0002fE-2r for guix-devel@gnu.org; Thu, 18 Aug 2016 07:11:09 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 0FE1338076A for ; Thu, 18 Aug 2016 13:11:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1471518662; x=1473333063; bh=Yqt9IWOXhNdDvF0Rs2WNbJquEIzfN57ouLcDmza91tI=; b=U7SYXGY9o+MV fIIh2XdFCxAcRjTRloLWey00WkdVzfLzQY9G8uwBxDpuJcO778Pv4/grgLlocXQN EsP/f2/rEdBwGDzA4qzg1iT72BJYMuCvECZ8p5Z0NXgaa4jgBThbBs9yFQgXhEpk Xm+Qi9dLgfVAZAxFTBWt5Ct1olrx2Rc= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id O5Edh8HR8yvx for ; Thu, 18 Aug 2016 13:11:02 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Thu, 18 Aug 2016 13:11:02 +0200 (CEST) Received: from localhost (141.80.180.135) by HTCATWO.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.294.0; Thu, 18 Aug 2016 13:11:01 +0200 From: Ricardo Wurmus To: Subject: [PATCH 2/2] gnu: Add r-bamsignals. Date: Thu, 18 Aug 2016 13:09:42 +0200 Message-ID: <20160818110942.28804-2-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.9.0 In-Reply-To: <20160818110942.28804-1-ricardo.wurmus@mdc-berlin.de> References: <20160818110942.28804-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4283-8.000.1202-22520.006 X-TM-AS-Result: No--0.955400-0.000000-31 X-TM-AS-MatchedID: 703786-704425-188019-702358-704496-701590-706817-139704-7 07570-862883-704568-706769-390306-701594-700323-701404-148004-148036-42000- 42003 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 141.80.25.30 X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.21 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+patchwork=sourceware.org@gnu.org Sender: "Guix-devel" * gnu/packages/bioinformatics.scm (r-bamsignals): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ade6e37..2bd71c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6350,6 +6350,36 @@ nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+))) +(define-public r-bamsignals + (package + (name "r-bamsignals") + (version "1.4.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bamsignals" version)) + (sha256 + (base32 + "1xqiqvg52p6fcvhr4146djbz79r3j1kmh75mq7rndwglmiybpwmy")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rcpp" ,r-rcpp) + ("r-rhtslib" ,r-rhtslib) + ("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) + (home-page "http://bioconductor.org/packages/bamsignals") + (synopsis "Extract read count signals from bam files") + (description + "This package allows to efficiently obtain count vectors from indexed bam +files. It counts the number of nucleotide sequence reads in given genomic +ranges and it computes reads profiles and coverage profiles. It also handles +paired-end data.") + (license license:gpl2+))) + (define-public emboss (package (name "emboss")