BioRuby patch updated. Pj.
>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: [email protected] From: Pjotr Prins <[email protected]> * 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
