BioRuby Shell

Build Status

bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an open source bioinformatics library for Ruby.

This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-shell and many more plugins are available at


bio-shell uses the bio gem. It will automatically be installed during the installation of bio-shell in normal cases.


Add this line to your application's Gemfile:

gem 'bio-shell'

And then execute:

$ bundle

Or install it yourself as:

$ gem install bio-shell


See BioRuby documentation at


To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to


Bug reports and pull requests are welcome on GitHub at


If you use this software, please cite one of