From patchwork Mon May 20 14:20:40 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?VG9kb3IgS29uZGnvv73vv70=?= X-Patchwork-Id: 14007 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 3B17C16FEC; Mon, 20 May 2019 15:40:41 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID, URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id EC30216FEC for ; Mon, 20 May 2019 15:40:39 +0100 (BST) Received: from localhost ([127.0.0.1]:36630 helo=lists.gnu.org) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hSjSs-00039X-Bq for patchwork@mira.cbaines.net; Mon, 20 May 2019 10:40:34 -0400 Received: from eggs.gnu.org ([209.51.188.92]:39631) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1hSjOW-0002BC-Ph for guix-patches@gnu.org; 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Mon, 20 May 2019 10:21:02 -0400 Received: from mail-40132.protonmail.ch ([185.70.40.132]:39504) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1hSj9w-0004cC-5u for guix-patches@gnu.org; Mon, 20 May 2019 10:21:00 -0400 Date: Mon, 20 May 2019 14:20:40 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=protonmail.com; s=default; t=1558362043; bh=BWynYmQPxyEu2n/kacONK+J8Hm63NAeGjc9hvyD4anM=; h=Date:To:From:Reply-To:Subject:Feedback-ID:From; b=gxwu04qr0x3cNbkZBsM7qiMktPsfzUV5gfLd9HPG5U3PaYjqWAMfs17PKb1FD7SBu 5e8FDrQlz4VTRA1IIYEuZfuSCeq4YYBAWsHA25uyZZ0L8rlgNlOJUxbU6peTjm9zh/ Z1BHPUc8nP+mimhNQ5Wq77Au0YEgpA4fqttSdBjk= From: Tk Message-ID: <0Wmcjgq-bpYQvMH_nhfAPRc8siXsADDFk0tfLvj-4onlp3m2aBbTJXEwrtdpbwWpgQnzn7-P8Hc6Gpq32B4rMmOq1GV8MkP75J2YJxSVMVs=@protonmail.com> Feedback-ID: H-HDHPDhHGpnHYYqEeeELdj-Ly2a7MuykpUWpBFgfQ1BCJpPfO2vKz9YpJUb7-VnGIEXLb5c-uxqytN6PxXV2Q==:Ext:ProtonMail MIME-Version: 1.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Mailman-Approved-At: Mon, 20 May 2019 10:35:09 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-Mailman-Approved-At: Mon, 20 May 2019 10:40:32 -0400 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: Tk Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches Hi, Some of us at ECI (Environmental Cheminformatics), LCSB, University of Luxembourg are in love with Scheme, GNU, Guile and Guix. At ECI, there is a lot of mass spectrometry going on and there are plenty of R tools -- some written by us -- to analyse and annotate such spectra. Anyway, this is our first contribution to Guix -- RMassBank (r-massbank package). I have decided to create a separate package group for mass-spectrometry and include r-massbank in it. I could imagine packages defined here to end up in chemistry.scm, or under a new subpath, chemistry/mass-spectrometry.scm. Once this first submission enters Guix, some more will follow. The packages themselves have been generated using `guix import cran -r --archive=bioconductor RMassBank` and minimally altered to build successfully and not bother guix lint too much. As this is my first contribution to guix, I am very much looking forward to feedback. Thanks, Todor --- gnu/packages/mass-spectrometry.scm | 163 +++++++++++++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100644 gnu/packages/mass-spectrometry.scm -- 2.21.0 diff --git a/gnu/packages/mass-spectrometry.scm b/gnu/packages/mass-spectrometry.scm new file mode 100644 index 0000000000..d2684856c1 --- /dev/null +++ b/gnu/packages/mass-spectrometry.scm @@ -0,0 +1,163 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2019 Todor Kondić +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages mass-spectrometry) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix utils) + #:use-module (guix build-system gnu) + #:use-module (guix build-system r) + #:use-module (gnu packages chemistry) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages statistics) + #:use-module (gnu packages cran) + #:use-module (gnu packages web) + #:use-module (gnu packages image) + #:use-module (gnu packages cran) + #:use-module (gnu packages) + #:use-module (srfi srfi-1)) + + + +(define-public r-fingerprint + (package + (name "r-fingerprint") + (version "3.5.7") + (source + (origin + (method url-fetch) + (uri (cran-uri "fingerprint" version)) + (sha256 + (base32 + "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic")))) + (build-system r-build-system) + (home-page + "https://cran.r-project.org/web/packages/fingerprint") + (synopsis + "Functions to Operate on Binary Fingerprint Data") + (description + "Functions to manipulate binary fingerprints of arbitrary length. A +fingerprint is represented by an object of S4 class 'fingerprint' which is +internally represented a vector of integers, such that each element represents +the position in the fingerprint that is set to 1. The bitwise logical +functions in R are overridden so that they can be used directly with +'fingerprint' objects. A number of distance metrics are also available (many +contributed by Michael Fadock). Fingerprints can be converted to Euclidean +vectors (i.e., points on the unit hypersphere) and can also be folded using +OR. Arbitrary fingerprint formats can be handled via line handlers. +Currently handlers are provided for CDK, MOE and BCI fingerprint data.") + (license (list gpl2+ gpl3+)))) + +(define-public r-cdklibs + (package + (name "r-cdklibs") + (version "2.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "rcdklibs" version)) + (sha256 + (base32 + "05g0y00bw1bqykfbwn4q42krwcfl50jcavaw7yyw9a5m34hvw0l8")))) + (build-system r-build-system) + (propagated-inputs `(("r-rjava" ,r-rjava))) + (home-page + "https://cran.r-project.org/web/packages/rcdklibs") + (synopsis "The CDK Libraries Packaged for R") + (description + "An R interface to the Chemistry Development Kit, a Java library for +chemoinformatics. Given the size of the library itself, this package is not +expected to change very frequently. To make use of the CDK within R, it is +suggested that you use the 'rcdk' package. Note that it is possible to +directly interact with the CDK using 'rJava'. However 'rcdk' exposes +functionality in a more idiomatic way. The CDK library itself is released as +LGPL and the sources can be obtained from .") + (license (list license:lgpl2.0 license:lgpl2.1 license:lgpl3)))) + +(define-public r-cdk + (package + (name "r-cdk") + (version "3.4.7.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "rcdk" version)) + (sha256 + (base32 + "1d08ajji631792b7fyfwzvcaswh8jlanfsxrj6c1wx7xh3qqpigg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fingerprint" ,r-fingerprint) + ("r-iterators" ,r-iterators) + ("r-itertools" ,r-itertools) + ("r-png" ,r-png) + ("r-cdklibs" ,r-cdklibs) + ("r-rjava" ,r-rjava) + ("r-knitr" ,r-knitr))) + (home-page + "https://cran.r-project.org/web/packages/rcdk") + (synopsis "Interface to the 'CDK' Libraries") + (description + "Allows the user to access functionality in the 'CDK', a Java framework +for chemoinformatics. This allows the user to load molecules, evaluate +fingerprints, calculate molecular descriptors and so on. In addition, the +'CDK' API allows the user to view structures in 2D.") + (license (list license:lgpl2.0 license:lgpl2.1 license:lgpl3)))) + +(define-public r-massbank + (package + (name "r-massbank") + (version "2.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RMassBank" version)) + (sha256 + (base32 + "1xdxrbkcggrlqx3h11w10vk18bjmdfs85j6rvy7yvqj7limsjp2j")))) + (properties `((upstream-name . "RMassBank"))) + (build-system r-build-system) + (inputs `(("openbabel" ,openbabel))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-digest" ,r-digest) + ("r-httr" ,r-httr) + ("r-msnbase" ,r-msnbase) + ("r-mzr" ,r-mzr) + ("r-cdk" ,r-cdk) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml) + ("r-markdown" ,r-markdown) + ("r-knitr" ,r-knitr) + ("r-yaml" ,r-yaml))) + (home-page + "https://bioconductor.org/packages/release/bioc/html/RMassBank.html") + (synopsis + "Workflow to process tandem MS files and build MassBank records") + (description + "Workflow to process tandem MS files and build MassBank records. +Functions include automated extraction of tandem MS spectra, formula +assignment to tandem MS fragments, recalibration of tandem MS spectra with +assigned fragments, spectrum cleanup, automated retrieval of compound +information from Internet databases, and export to MassBank records.") + (license license:artistic2.0)))