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[PATCH] gnu: Add ruby-libxml and bioruby.
From: |
Pjotr Prins |
Subject: |
[PATCH] gnu: Add ruby-libxml and bioruby. |
Date: |
Tue, 15 Sep 2015 14:15:16 +0200 |
User-agent: |
Heirloom mailx 12.5 6/20/10 |
* 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
- [PATCH] gnu: Add ruby-libxml and bioruby.,
Pjotr Prins <=
- Re: [PATCH] gnu: Add ruby-libxml and bioruby., Thompson, David, 2015/09/15
- Re: [PATCH] gnu: Add ruby-libxml and bioruby., Pjotr Prins, 2015/09/15
- Re: [PATCH] gnu: Add ruby-libxml and bioruby., Thompson, David, 2015/09/15
- Re: [PATCH] gnu: Add ruby-libxml and bioruby., Pjotr Prins, 2015/09/17
- Re: [PATCH] gnu: Add ruby-libxml, Pjotr Prins, 2015/09/17
- Re: [PATCH] gnu: Add ruby-libxml, Thompson, David, 2015/09/19
- Re: [PATCH] gnu: Add ruby-libxml and bioruby., Pjotr Prins, 2015/09/17
- Re: [PATCH] gnu: Add ruby-libxml and bioruby., Thompson, David, 2015/09/19
Re: [PATCH] gnu: Add ruby-libxml and bioruby., Pjotr Prins, 2015/09/15