README.rdoc - README for BioRuby
Copyright (C) 2001-2007 Toshiaki Katayama <firstname.lastname@example.org>, Copyright (C) 2008 Jan Aerts <email@example.com> Copyright (C) 2011-2015 Naohisa Goto <firstname.lastname@example.org>
The Ruby License
The above statement is limited to this file. See below about BioRuby's copyright and license.
Copyright (C) 2001-2012 Toshiaki Katayama <email@example.com>
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 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
This file. General information and installation procedure.
News and important changes in this release.
Known issues and bugs in BioRuby.
News and incompatible changes from 1.4.2 to 1.4.3.
News and incompatible changes from 1.4.1 to 1.4.2.
News and incompatible changes from 1.4.0 to 1.4.1.
News and incompatible changes from 1.3.1 to 1.4.0.
News and incompatible changes from 1.2.1 to 1.3.0.
News and incompatible changes from 0.6.4 to 1.2.1.
Tutorials and other useful information
HTML version of Tutorial.rd.
History of changes.
changes from 1.4.2 to 1.4.3.
changes before 1.4.2.
changes before 1.3.1.
Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
Documents written in Japanese
BioRuby Tutorial written in Japanese.
HTML version of Tutorial.rd.ja.
In sample/, There are many sample codes and demo scripts.
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.
Mirror site is available, hosted on Open Bioinformatics Foundation (OBF).
WHERE TO OBTAIN
The stable release is freely available from the BioRuby website.
RubyGems (packaging system for Ruby) version of the BioRuby package is also available for easy installation.
If you need the latest development version, this is provided at
and can be obtained by the following procedure:
% git clone git://github.com/bioruby/bioruby.git
Ruby 1.8.7 or later (except Ruby 1.9.0) – www.ruby-lang.org/
Ruby 2.1.6 or later, or Ruby 2.2.2 or later is recommended.
This is the final version running on Ruby 1.8, tested with Ruby1.8.7-p374.
See KNOWN_ISSUES.rdoc for Ruby version specific problems.
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 following web sites.
For faster parsing of the BLAST XML output format:
Creating faster flatfile index using Berkley DB:
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):
For parsing PhyloXML format files:
INSTALL by using RubyGems (recommended)
If you are using RubyGems, just type
% gem install bio
Alternatively, manually download bio-X.X.X.gem from bioruby.org/archive/ 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.
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
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.
If you want to use the OBDA (Open Bio Database Access) to obtain database entries, copy a sample configuration file in the BioRuby distribution
/etc/bioinformatics/seqdatabase.ini (system wide configuration)
~/.bioinformatics/seqdatabase.ini (personal configuration)
and change the contents according to your preference. For more information on the OBDA, see obda.open-bio.org/ .
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.
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'
Many plugins (called Biogem) are now available. See biogems.info/ for list of plugins and related software utilizing BioRuby.
To develop your own plugin, see “Plugins” pages of BioRuby Wiki.
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 “setup” developed by Minero Aoki (i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1.
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.
Current staff of the BioRuby project can be reached by sending e-mail to <firstname.lastname@example.org>.