gnu: Add bioruby.
* gnu/packages/bioinformatics.scm (bioruby): New variable.
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@ -2700,3 +2700,46 @@ position for indels. Bio-locus allows users to store this chr+pos or
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chr+pos+alt information in a database.")
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(home-page "https://github.com/pjotrp/bio-locus")
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(license license:expat)))
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(define-public bioruby
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(package
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(name "bioruby")
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(version "1.5.0")
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(source
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(origin
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(method url-fetch)
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(uri (rubygems-uri "bio" version))
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(sha256
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(base32
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"01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
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(build-system ruby-build-system)
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(propagated-inputs
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`(("ruby-libxml" ,ruby-libxml)))
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(native-inputs
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`(("which" ,which))) ; required for test phase
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-before 'build 'patch-test-command
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(lambda _
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(substitute* '("test/functional/bio/test_command.rb")
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(("/bin/sh") (which "sh")))
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(substitute* '("test/functional/bio/test_command.rb")
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(("/bin/ls") (which "ls")))
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(substitute* '("test/functional/bio/test_command.rb")
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(("which") (which "which")))
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(substitute* '("test/functional/bio/test_command.rb",
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"test/data/command/echoarg2.sh")
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(("/bin/echo") (which "echo")))
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#t)))))
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(synopsis "Ruby library, shell and utilities for bioinformatics")
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(description "BioRuby comes with a comprehensive set of Ruby development
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tools and libraries for bioinformatics and molecular biology. BioRuby has
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components for sequence analysis, pathway analysis, protein modelling and
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phylogenetic analysis; it supports many widely used data formats and provides
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easy access to databases, external programs and public web services, including
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BLAST, KEGG, GenBank, MEDLINE and GO.")
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(home-page "http://bioruby.org/")
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;; Code is released under Ruby license, except for setup
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;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
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(license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
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