BioRuby

Software Summary

Mesabi

Default Module:

Other Modules Available:

Last Updated On:

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

Other Modules Available:

Last Updated On:

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

1.4.2

Other Versions Available:

1.4.2

Last Updated On:

Wednesday, December 7, 2016

Last Updated On:

Wednesday, December 7, 2016

Support Level:

Secondary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Genetics

Software Description

BioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.

Software Documentation

Software Documentation Tabs

General Linux

To run this softwar in a Linux environment run the commands:

module load bioruby
bioruby

BioRuby has a number of modules that can be used in your Ruby scripts. Writing Ruby scripts is outside the scope of this document, but below is a small example of how to read and print sequence data from a file:

#!/usr/bin/env ruby
require 'bio'
file=Bio::FastaFormat.open(ARGV.shift)
file.each_entry do |f|
puts "Sequence: " + f.seq
end

More information, including documentation and tutorials, may be found at the the BioRuby homepage.

Additional Information