BioRuby Shell

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 biogems.info.

Requirements

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

Installation

Add this line to your application's Gemfile:

gem 'bio-shell'

And then execute:

$ bundle

Or install it yourself as:

$ gem install bio-shell

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-shell

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