BioRuby Executables

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bio-executables is a collection of miscellaneous utilities for bioinformatics that were formerly part of the BioRuby core ("bio" gem). Because of reducing complexity, they were moved to this gem.

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-executables and many more plugins are available at


bio-executables uses bio and bio-old-biofetch-emulator gems. They will automatically be installed during the installation of bio-executables in normal cases.


Add this line to your application's Gemfile:

gem 'bio-executables'

And then execute:

$ bundle

Or install it yourself as:

$ gem install bio-executables


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