From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus 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> References: <20160818110942.28804-1-ricardo.wurmus@mdc-berlin.de> Mime-Version: 1.0 Content-Type: text/plain Return-path: 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) 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) In-Reply-To: <20160818110942.28804-1-ricardo.wurmus@mdc-berlin.de> 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+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: guix-devel@gnu.org * 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") -- 2.9.0