BioRuby Executables

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 biogems.info.

Requirements

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

Installation

Add this line to your application's Gemfile:

gem 'bio-executables'

And then execute:

$ bundle

Or install it yourself as:

$ gem install bio-executables

Usage

See BioRuby documentation at https://github.com/bioruby/documentation

Development

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 rubygems.org.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/bioruby/bioruby-executables

Cite

If you use this software, please cite one of

• BioRuby: bioinformatics software for the Ruby programming language
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics