# README.rdoc

Path: | README.rdoc
Last Update: | Sat Sep 29 00:26:22 +0000 2012

# BioRuby

Copyright (C) 2001-2012 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

See RELEASE_NOTES.rdoc for news and important changes in this version.

### Documents in this distribution

#### Release notes, important changes and issues

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-1.4.2.rdoc: | News and incompatible changes from 1.4.1 to 1.4.2.
doc/RELEASE_NOTES-1.4.1.rdoc: | News and incompatible changes from 1.4.0 to 1.4.1.
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.
doc/ChangeLog-before-1.4.2: | changes before 1.4.2.
doc/ChangeLog-before-1.3.1: | changes before 1.3.1.
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.

#### Sample codes

In sample/, There are many sample codes and demo scripts.

### 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/

Mirror site is available, hosted on Open Bioinformatics Foundation (OBF).

- bioruby.open-bio.org/

## WHERE TO OBTAIN

### WWW

The stable release is freely available from the BioRuby website.

- bioruby.org/archive/

### RubyGems

RubyGems (packaging system for Ruby) 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

## REQUIREMENTS

- Ruby 1.8.6 or later (except Ruby 1.9.0) — www.ruby-lang.org/
  - Ruby 1.9.3-p194 or later, or Ruby 1.8.7-p358 or later is recommended.
  - See KNOWN_ISSUES.rdoc for Ruby version specific problems.

## OPTIONAL REQUIREMENTS

Some optional libraries can be utilized to extend BioRuby‘s functionality. If your needs meets the following conditions, install them by using RubyGems, or download and install from the "Ruby Application Archive" (RAA) at raa.ruby-lang.org/, RubyForge at rubyforge.org/, GitHub at github.com/, or the following web sites.

For faster parsing of the BLAST XML output format:

- RAA:xmlparser
  - For Ruby 1.8: gem install xmlparser
  - For Ruby 1.9: www.yoshidam.net/Ruby.html#xmlparser
  - In both cases, The Expat XML Parser and C compiler will be required.

Creating faster flatfile index using Berkley DB:

- GitHub:ruby-bdb (which took over RAA:bdb) (No RubyGems available)
  - Oracle Berkeley DB and C compiler will be required.

Accessing BioSQL database created by other Open Bio* libraries:

- gem install activerecord and at least one driver (or adapter):
  - gem install mysql or gem install mysql2
  - gem install pg
  - gem install sqlite-ruby or gem install sqlite3
  - gem install activerecord-oracle_enhanced-adapter

For parsing PhyloXML format files:

- gem install libxml-ruby
  - GNOME Libxml2 XML toolkit and C compiler will be required.

(Only for Ruby 1.9.x) For using SOAP web services e.g. KEGG API:

- gem install soap4r-ruby1.9
  - For Ruby 1.8.x, SOAP4R is bundled within the Ruby 1.8.x release.

## INSTALL

### INSTALL by using RubyGems (recommended)

If you are using RubyGems, just type

      % gem install bio

Alternatively, manually download bio-X.X.X.gem from rubyforge.org/projects/bioruby/ and install it by using gems command.

RubyGems is bundled with Ruby 1.9.1 or later. For Ruby 1.8.7 or earlier, download and install RubyGems from rubygems.org/ .

### INSTALL without RubyGems

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

      % ruby setup.rb --help

for more details.

### Running self-test

To check if bioruby works fine on a machine, self-test codes are bundled. Note that some tests may need internet connection.

To run tests,

     % ruby test/runner.rb

If you are using Ruby 1.8.x and you want to use components installed by using RubyGems, explicit loading of RubyGems may be needed.

     % ruby -rubygems test/runner.rb

Alternatively, testrb, the test runner command of ruby, can be used.

     % testrb test/

With testrb, you can select tests to run, for example,

     % testrb test/unit

For those familiar with Rake,

     % rake test

also works.

Before reporting test failure, please check KNOWN_ISSUES.rdoc about known platform-dependent issues. We are happy if you write patches to solve the issues.

## 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 on Ruby 1.8.x

With RubyGems on Ruby 1.8.x, you may need to load ‘rubygems’ library before using ‘bio’. This may not be needed, depending on settings of Ruby.

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

## PLUGIN (Biogem)

Many plugins (called Biogem) are now available. See biogems.info/ for list of plugins and related software utilizing BioRuby.

- biogems.info/

To develop your own plugin, see "Plugins" pages of BioRuby Wiki.

- bioruby.open-bio.org/wiki/Plugins

## 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.

## REFERENCE

If you use BioRuby in academic research, please consider citing the following publication.

- BioRuby: Bioinformatics software for the Ruby programming language. Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama. Bioinformatics (2010) 26(20): 2617-2619.
  - doi: 10.1093/bioinformatics/btq475
  - PMID: 20739307

## CONTACT

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

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