From mboxrd@z Thu Jan 1 00:00:00 1970 From: Pjotr Prins Subject: [PATCH] gnu: Add ruby-libxml and bioruby. Date: Tue, 15 Sep 2015 14:15:16 +0200 Message-ID: <55f80bd4.pVH9EKb+UmuOGLkt%pjotr.public12@thebird.nl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:38583) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZbpAn-0005gR-Sw for guix-devel@gnu.org; Tue, 15 Sep 2015 08:17:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZbpAj-0000Uw-Tt for guix-devel@gnu.org; Tue, 15 Sep 2015 08:17:21 -0400 Received: from mail.thebird.nl ([95.154.246.10]:54176) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZbpAj-0000Uf-LR for guix-devel@gnu.org; Tue, 15 Sep 2015 08:17:17 -0400 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel * gnu/packages/ruby.scm (ruby-libxml): New variable. * gnu/packages/bioinformatics.scm (bioruby): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/ruby.scm | 26 +++++++++++++++++++++++ 2 files changed, 73 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f34211..b297ef2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2642,3 +2642,50 @@ position for indels. Bio-locus allows users to store this chr+pos or chr+pos+alt information in a database.") (home-page "https://github.com/pjotrp/bio-locus") (license license:expat))) + +(define-public bioruby + (package + (name "bioruby") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio" version)) + (sha256 + (base32 + "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc")))) + (build-system ruby-build-system) + (native-inputs `(("ruby-libxml" ,ruby-libxml))) + (inputs + `(("coreutils" ,coreutils) ; required for /bin/echo in tests + ("which" ,which))) ; required for tests + (arguments + `(#:phases + (alist-cons-before + 'build 'replace-sh-commands + (lambda _ + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/sh") (which "sh"))) + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/ls") (which "ls"))) + (substitute* '("test/functional/bio/test_command.rb") + (("which") (which "which"))) + (substitute* '("test/functional/bio/test_command.rb", + "test/data/command/echoarg2.sh") + (("/bin/echo") (which "echo")))) + %standard-phases))) + (synopsis + "Ruby library, shell and utilities for bioinformatics") + (description + "BioRuby comes with a comprehensive set of free development +tools and libraries for bioinformatics and molecular biology, for the +Ruby programming language. BioRuby has components for sequence +analysis, pathway analysis, protein modelling and phylogenetic +analysis; it supports many widely used data formats and provides easy +access to databases, external programs and public web services, +including BLAST, KEGG, GenBank, MEDLINE and GO.") + (home-page "http://bioruby.org/") + ;; Code is released under Ruby license, except for setup + ;; (LGPLv2.1+), scripts in samples (GPL2 and GPL2+) + (license (list license:ruby license:lgpl2.1+ license:gpl2 + license:gpl2+ )))) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index ee0acc8..1ca5f96 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -465,6 +465,32 @@ extensions.") (home-page "http://codeforpeople.com/lib/ruby/orderedhash/") (license license:public-domain))) +(define-public ruby-libxml + (package + (name "ruby-libxml") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "libxml-ruby" version)) + (sha256 + (base32 + "1dhjqp4r9vkdp00l6h1cj8qfndzxlhlxk6b9g0w4v55gz857ilhb")))) + (build-system ruby-build-system) + (inputs `(("zlib" ,zlib) + ("libxml2" ,libxml2))) + (arguments + '(#:tests? #f ; tests need installation of build first + #:gem-flags (list "--" + (string-append "--with-xml2-include=" + (assoc-ref %build-inputs "libxml2") + "/include/libxml2" )))) + (synopsis "Ruby bindings for the GNOME Libxml2 XML toolkit") + (description "The Libxml-Ruby project provides Ruby language +bindings for the GNOME Libxml2 XML toolkit.") + (home-page "http://xml4r.github.com/libxml-ruby") + (license license:expat))) + (define-public ruby-xml-simple (package (name "ruby-xml-simple") -- 2.4.3