From: Pjotr Prins <pjotr.public12@thebird.nl>
To: "Thompson, David" <dthompson2@worcester.edu>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH] gnu: Add ruby-libxml and bioruby.
Date: Thu, 17 Sep 2015 08:17:50 +0200 [thread overview]
Message-ID: <20150917061750.GA10616@thebird.nl> (raw)
In-Reply-To: <CAJ=RwfbOP6Fuy4Km7mXVEub3W1HRVr2dBUQo0krr2pQfeiqyMQ@mail.gmail.com>
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BioRuby patch updated.
Pj.
[-- Attachment #2: 0001-gnu-Add-ruby-libxml-and-bioruby.patch --]
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From dd1fb03349d2ba2e7f36252d68f3de11f21b8866 Mon Sep 17 00:00:00 2001
Date: Thu, 17 Sep 2015 06:17:44 +0000
Subject: [PATCH] gnu: Add ruby-libxml and bioruby.
To: guix-devel@gnu.org
From: Pjotr Prins <pjotr.public12@thebird.nl>
* gnu/packages/bioinformatics.scm (bioruby): New variable.
---
gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f34211..5df77a9 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)
+ (propagated-inputs `(("ruby-libxml" ,ruby-libxml)))
+ (native-inputs
+ `(("which" ,which))) ; required for test phase
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before
+ 'build 'patch-test-command
+ (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")))
+ #t)))))
+ (synopsis
+ "Ruby library, shell and utilities for bioinformatics")
+ (description
+ "BioRuby comes with a comprehensive set of 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+) and scripts in samples (which have GPL2 and GPL2+)
+ (license (list license:ruby license:lgpl2.1+ license:gpl2
+ license:gpl2+ ))))
--
2.4.3
next prev parent reply other threads:[~2015-09-17 6:19 UTC|newest]
Thread overview: 12+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-09-15 12:15 [PATCH] gnu: Add ruby-libxml and bioruby Pjotr Prins
2015-09-15 12:58 ` Thompson, David
2015-09-15 13:19 ` Pjotr Prins
2015-09-15 14:39 ` Thompson, David
2015-09-17 5:24 ` Pjotr Prins
2015-09-17 5:37 ` [PATCH] gnu: Add ruby-libxml Pjotr Prins
2015-09-19 16:34 ` Thompson, David
2015-09-17 6:17 ` Pjotr Prins [this message]
2015-09-19 16:42 ` [PATCH] gnu: Add ruby-libxml and bioruby Thompson, David
2015-09-15 13:44 ` Pjotr Prins
-- strict thread matches above, loose matches on Subject: below --
2015-09-15 12:16 Pjotr Prins
2015-09-15 12:24 ` Pjotr Prins
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