bio-biosql

Bio::SQL -- BioRuby BioSQL Plugin

IMPORTANT NOTICE: This package is preliminary experimental state. It may not work as expected. Please fix bugs and report to us.

bio-biosql is a BioSQL plugin for BioRuby, an open source bioinformatics library for Ruby.

BioSQL is a set of SQL schema for storing biological sequences with meta-data. BioSQL supports major open-source database engines. See BioSQL Documentation for details.

This code written in Ruby has historically been part of the core BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-biosql and many more plugins are available at biogems.info.

This code was initially written by Toshiaki Katayama. Raoul Jean Pierre Bonnal greatly improved the code with introducing ActiveRecord. For details of development, see github.com/helios/bioruby, github.com/bioruby/bioruby, and the BioRuby mailing list archives.

Installation

Add this line to your application's Gemfile:

gem 'bio-biosql'

And then execute:

$ bundle

Or install it yourself as:

$ gem install bio-biosql

Requirements

In addition to the dependency written in Gemfile, at least one ActiveRecord adapter will be needed.

• pg
• sqlite-ruby
• sqlite3
• mysql
• mysql2
• activerecord-oracle_enhanced-adapter

TODO: Please test Bio::SQL with above adapters.

Usage

TODO: Write usage instructions here

Contributing

1. Fork it ( https://github.com/bioruby/bioruby-biosql/fork )
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request