Naohisa Goto edited this page Jun 14, 2016 · 1 revision

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
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:

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

% gem -v

% sudo gem update --system
Updating RubyGems...
Bulk updating Gem source index for:
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

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)
  ==> #<Bio::Sequence:0x117de40 @seq="atgcatgcatgcatgcatgcatgcatgcatgcatgcatgc", @moltype=Bio::Sequence::NA>
bioruby> seq.randomize
  ==> "ttcgagaacaccgcgatcgttgcaagattcgttatcaggc"
bioruby> seq.randomize.translate
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  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

>>>  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
=> 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
=> 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
** 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
** 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.


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

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