# README.rdoc

Path: | README.rdoc
Last Update: | Wed Jan 05 06:23:29 +0000 2011

# BioRuby

Copyright (C) 2001-2010 Toshiaki Katayama <k@bioruby.org>

BioRuby is an open source Ruby library for developing bioinformatics software. Object oriented scripting language Ruby has many features suitable for bioinformatics research, for example, clear syntax to express complex objects, regular expressions for text handling as powerful as Perl‘s, a wide variety of libraries including web service etc. As the syntax of the Ruby language is simple and very clean, we believe that it is easy to learn for beginners, easy to use for biologists, and also powerful enough for the software developers.

In BioRuby, you can retrieve biological database entries from flat files, internet web servers and local relational databases. These database entries can be parsed to extract information you need. Biological sequences can be treated with the fulfilling methods of the Ruby‘s String class and with regular expressions. Daily tools like Blast, Fasta, Hmmer and many other software packages for biological analysis can be executed within the BioRuby script, and the results can be fully parsed to extract the portion you need. BioRuby supports major biological database formats and provides many ways for accessing them through flatfile indexing, SQL, web services etc. Various web services including KEGG API can be easily utilized by BioRuby.

## FOR MORE INFORMATION

### Documents in this distribution

#### General information

README.rdoc: | This file. General information and installation procedure.
RELEASE_NOTES.rdoc: | News and important changes in this release.
KNOWN_ISSUES.rdoc: | Known issues and bugs in BioRuby.
doc/RELEASE_NOTES-1.4.0.rdoc: | News and incompatible changes from 1.3.1 to 1.4.0.
doc/Changes-1.3.rdoc: | News and incompatible changes from 1.2.1 to 1.3.0.
doc/Changes-0.7.rd: | News and incompatible changes from 0.6.4 to 1.2.1.

#### Tutorials and other useful information

doc/Tutorial.rd: | BioRuby Tutorial.
doc/Tutorial.rd.html: | HTML version of Tutorial.rd.
doc/KEGG_API.rd: | Documents about KEGG API, including usage of Bio::KEGG::API.

#### BioRuby development

ChangeLog: | History of changes.
README_DEV.rdoc: | Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.

#### Documents written in Japanese

doc/Tutorial.rd.ja: | BioRuby Tutorial written in Japanese.
doc/Tutorial.rd.ja.html: | HTML version of Tutorial.rd.ja.
doc/KEGG_API.rd.ja: | Japanese translation of KEGG_API.rd.

### WWW

BioRuby‘s official website is at bioruby.org/. You will find links to related resources including downloads, mailing lists, Wiki documentation etc. in the top page.

- bioruby.org/

## WHERE TO OBTAIN

### WWW

The stable release is freely available from the BioRuby website.

- bioruby.org/archive/

### RubyGems

RubyGems version of the BioRuby package is also available for easy installation.

- rubyforge.org/projects/bioruby/

### git

If you need the latest development version, this is provided at

- github.com/bioruby/bioruby

and can be obtained by the following procedure:

      % git clone git://github.com/bioruby/bioruby.git

#### CVS

CVS is now deprecated as source control has moved to github. Please use git instead of CVS. For historical purposes: the anonymous CVS was provided at

- cvs.bioruby.org/

and could be obtained by the following procedure.

      % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
      CVS password: cvs (login with a password 'cvs' for the first time)
      % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby

## REQUIREMENTS

- Ruby 1.8.2 or later (except Ruby 1.9.0) — www.ruby-lang.org/
  - Ruby 1.8.7-p174 or later, or Ruby 1.8.6-p383 or later is recommended.
  - Not yet fully ready with Ruby 1.9, although many components can now work in Ruby 1.9.1 and Ruby 1.9.2.

## OPTIONAL REQUIREMENTS

Some optional libraries can be utilized to extend BioRuby‘s functionality. If your needs meets the following conditions, install them from the "Ruby Application Archive" at raa.ruby-lang.org/, RubyForge at rubyforge.org/, or the following web sites.

For faster parsing of the BLAST XML output format:

- RAA:xmlparser

Creating faster flatfile index using Berkley DB:

- RAA:bdb

Accessing BioSQL database created by other Open Bio* libraries:

- RubyForge:ActiveRecord and at least one driver (or adapter) from RubyForge:MySQL/Ruby, RubyForge:postgres-pr, or RubyForge:ActiveRecord Oracle enhanced adapter.
- For BioRuby 1.2.1 or older version, RubyForge:Ruby/DBI and at least one driver from MySQL/Ruby, postgres-pr, or RubyForge:ruby-oci8 (note that ruby-oci8 can only work with ruby-dbi 0.2.2).

For parsing PhyloXML format files:

- RubyForge:libxml-ruby (Ruby language bindings for the GNOME Libxml2 XML toolkit)

## INSTALL

In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb as follows:

      % su
      # ruby setup.rb

These simple step installs this program under the default location of Ruby libraries. You can also install files into your favorite directory by supplying setup.rb some options. Try "ruby setup.rb —help".

If your operating system supports ‘sudo’ command (such as Mac OS X), try the following procedure instead of the above.

      % sudo ruby setup.rb

For older version users: "install.rb" is now renamed to "setup.rb". The options "config", "setup", and "install" are still available.

      % ruby setup.rb config
      % ruby setup.rb setup
      % su
      # ruby setup.rb install

You can run tests by

      % ruby setup.rb test

and run

      % ruby setup.rb --help

for more details.

### RubyGems

If you are using RubyGems, just type

      % gems install bio

## SETUP

If you want to use the OBDA (Open Bio Database Access) to obtain database entries, copy a sample configuration file in the BioRuby distribution

      bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini

to

      /etc/bioinformatics/seqdatabase.ini   (system wide configuration)

or

      ~/.bioinformatics/seqdatabase.ini     (personal configuration)

and change the contents according to your preference. For more information on the OBDA, see obda.open-bio.org/ .

## USAGE

You can load all BioRuby classes just by requiring ‘bio.rb’. All the BioRuby classes and modules are located under the module name ‘Bio’ to separate the name space.

      #!/usr/bin/env ruby
      require 'bio'

You can also read other documentation in the ‘doc’ directory.

      bioruby-x.x.x/doc/

### RubyGems

With RubyGems, you need to load ‘rubygems’ library before using ‘bio’.

      #!/usr/bin/env ruby
      require 'rubygems'
      require 'bio'

With old version of RubyGems, use ‘require_gem’ which was deprecated in RubyGems 0.9.0 and removed in RubyGems 1.0.1.

      #!/usr/bin/env ruby
      require 'rubygems'
      require_gem 'bio'

## LICENSE

BioRuby can be freely distributed under the same terms as Ruby. See the file COPYING (or COPYING.ja written in Japanese).

As written in the file COPYING, see the file LEGAL for files distributed under different license. For example, setup.rb which comes from RAA:setup developed by Minero Aoki (i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1.

## CONTACT

Current staff of the BioRuby project can be reached by sending e-mail to <staff@bioruby.org>.

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