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.
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 https://github.com/bioruby/documentation
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.
Bug reports and pull requests are welcome on GitHub at https://github.com/bioruby/bioruby-shell
If you use this software, please cite one of