From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH 09/16] gnu: Add r-mzr. Date: Tue, 17 Jan 2017 15:11:34 +0100 Message-ID: <20170117141141.11694-10-rekado@elephly.net> References: <20170117141141.11694-1-rekado@elephly.net> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40017) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cTUUy-0007MQ-DH for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:33 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cTUUv-0006UM-5w for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:32 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:21001) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cTUUu-0006TD-Uo for guix-devel@gnu.org; Tue, 17 Jan 2017 09:12:29 -0500 In-Reply-To: <20170117141141.11694-1-rekado@elephly.net> 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-mzr): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4a1bd0196..51660026e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8248,3 +8248,35 @@ as allowing spectra with different resolutions.") "This package provides S4 generic functions needed by Bioconductor proteomics packages.") (license license:artistic2.0))) + +(define-public r-mzr + (package + (name "r-mzr") + (version "2.8.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "mzR" version)) + (sha256 + (base32 + "0ipmhg6l3pf648rdx5g2ha7l5ppd3cja6afxhdw76x8ga3633x0r")))) + (properties `((upstream-name . "mzR"))) + (build-system r-build-system) + (inputs + `(("netcdf" ,netcdf))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-protgenerics" ,r-protgenerics) + ("r-rcpp" ,r-rcpp) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://github.com/sneumann/mzR/") + (synopsis "Parser for mass spectrometry data files") + (description + "The mzR package provides a unified API to the common file formats and +parsers available for mass spectrometry data. It comes with a wrapper for the +ISB random access parser for mass spectrometry mzXML, mzData and mzML files. +The package contains the original code written by the ISB, and a subset of the +proteowizard library for mzML and mzIdentML. The netCDF reading code has +previously been used in XCMS.") + (license license:artistic2.0))) -- 2.11.0