BioRubyOnRails

This page describes how to use BioRuby with your Rails application.

BioRuby comes with an interactive shell which can be used in a console or in a web browser as a Rails plugin.



How to use BioRuby on Rails
Installing the BioRuby 1.3.0 release as a Ruby gems package.

% sudo gem install bio Password: Successfully installed bio-1.3.0 1 gem installed Installing ri documentation for bio-1.3.0... Installing RDoc documentation for bio-1.3.0...

If your gem stick at the following message

Bulk updating Gem source index for: http://gems.rubyforge.org

and took very long time to find the BioRuby gem, you'd better to update the RubyGems itself.

% gem -v 1.0.1 % sudo gem update --system Updating RubyGems... Bulk updating Gem source index for: http://gems.rubyforge.org Attempting remote update of rubygems-update Successfully installed rubygems-update-1.3.1 1 gem installed Updating version of RubyGems to 1.3.1 Installing RubyGems 1.3.1 : RubyGems system software updated % gem -v 1.3.1

OK. Test the BioRuby shell in a console.

% bioruby Loading config (/Users/xxx/.bioruby/shell/session/config) ... done Loading object (/Users/xxx/.bioruby/shell/session/object) ... done Loading history (/Users/xxx/.bioruby/shell/session/history) ... done . . . B i o R u b y  i n   t h e   s h e l l. . . Version : BioRuby 1.3.0 / Ruby 1.8.6 bioruby> seq = getseq("atgc" * 10) ==> # bioruby> seq.randomize ==> "ttcgagaacaccgcgatcgttgcaagattcgttatcaggc" bioruby> seq.randomize.translate ==> "HFGLYRN*RGQRL" bioruby> exit . . . B i o R u b y  i n   t h e   s h e l l. . . Saving history (/Users/full/.bioruby/shell/session/history) ... done Saving object (/Users/full/.bioruby/shell/session/object) ... done Saving config (/Users/full/.bioruby/shell/session/config) ... done

Create an Rails project (you can also use existing Rails application as well).

% rails -v Rails 1.2.6 % rails hoge create create app/controllers :     create  log/test.log

Activate the BioRuby shell as a Rails plugin.

% bioruby --rails hoge Creating directory (/Users/ktym/hoge/shell/session) ... done Creating directory (/Users/ktym/hoge/shell/plugin) ... done Creating directory (/Users/ktym/hoge/data) ... done Installing Rails plugin for BioRuby shell ...      exists  app/controllers exists app/helpers create app/views/bioruby exists app/views/layouts create public/images/bioruby exists public/stylesheets create app/controllers/bioruby_controller.rb      create  app/helpers/bioruby_helper.rb      create  app/views/bioruby/_methods.rhtml create app/views/bioruby/_classes.rhtml create app/views/bioruby/_modules.rhtml create app/views/bioruby/_log.rhtml create app/views/bioruby/_variables.rhtml create app/views/bioruby/commands.rhtml create app/views/bioruby/history.rhtml create app/views/bioruby/index.rhtml create app/views/layouts/bioruby.rhtml create public/images/bioruby/spinner.gif create public/images/bioruby/gem.png create public/images/bioruby/link.gif create public/images/bioruby/bg.gif create public/stylesheets/bioruby.css done >>> >>> open http://localhost:3000/bioruby >>> (You can change the port number by adding "-- -p 4000" option) . . . B i o R u b y  i n   t h e   s h e l l. . . Version : BioRuby 1.3.0 / Ruby 1.8.7 => Booting WEBrick... => Rails application started on http://0.0.0.0:3000 => Ctrl-C to shutdown server; call with --help for options [2009-02-25 01:19:29] INFO WEBrick 1.3.1 [2009-02-25 01:19:29] INFO ruby 1.8.7 (2008-06-09) [i686-darwin9.3.0] [2009-02-25 01:19:29] INFO WEBrick::HTTPServer#start: pid=11036 port=3000

You may see the different message as follows if you have installed a Mongrel web server for Rails.

. . . B i o R u b y  i n   t h e   s h e l l. . . Version : BioRuby 1.3.0 / Ruby 1.8.6 ./config/boot.rb:20:Warning: Gem::SourceIndex#search support for String patterns is deprecated => Booting Mongrel (use 'script/server webrick' to force WEBrick) => Rails application starting on http://0.0.0.0:3000 => Call with -d to detach => Ctrl-C to shutdown server /Library/Ruby/Gems/1.8/gems/mongrel-1.1.5/bin/mongrel_rails:60: warning: conflicting chdir during another chdir block
 * Starting Mongrel listening at 0.0.0.0:3000
 * Starting Rails with development environment...
 * Rails loaded.
 * Loading any Rails specific GemPlugins
 * Signals ready. TERM => stop.  USR2 => restart.  INT => stop (no restart).
 * Rails signals registered. HUP => reload (without restart).  It might not work well.
 * Mongrel 1.1.5 available at 0.0.0.0:3000
 * Use CTRL-C to stop.

Anyway, that's it. You are ready to use the BioRuby shell on Rails now.

Open the following URL in your web browser.

http://localhost:3000/bioruby

You can now able to use all of Ruby and BioRuby functionalities even with your Rails models in your browser. Enjoy!