Monday, October 12, 2009

About BioRuby


We always read the documentation first.
There is an installation guide too.

Installation using gemThe gem installation is recommended.
On Windows:
> gem update --system
> gem install bio
> gem update bio
> gem install chemruby-1.1.9.gem
> gem update chemruby
On Linux:
&] sudo gem update --system ; sudo gem install bio ; sudo gem update bio

There is a sourceforge download if you want a gem file.

Installation from source for BioRuby and ChemRubyThere is an archive download.

&] sudo cp ~/Downloads/bioruby-1*tar.gz /opt ; cd /opt
&] sudo tar -zxf bioruby-1*tar.gz ; cd bioruby ; sudo chmod -R +x *
&] ruby setup.rb -help
&] sudo ruby setup.rb
&] ruby setup.rb config
&] ruby setup.rb setup
&] sudo ruby setup.rb install
&] ruby setup.rb test

&] sudo cp ~/Downloads/chemruby-1.0.0.tar.gz /opt ; cd /opt
&] sudo tar -zxf chemruby-1.0.0.tar.gz ; cd chemruby-1.0.0 ; sudo chmod -R +x *
&] ruby setup.rb --help
&] sudo ruby setup.rb
&] sudo ruby setup.rb config
&] ruby setup.rb setup
&] sudo ruby setup.rb install
&] ruby setup.rb test

Using downloaded gem:
&] sudo gem install chemruby-1.1.9.gem ; sudo gem update chemruby

Installation of optional requirements in RAA (Ruby Application Archive)The RAA setup
&] sudo cp ~/Downloads/setup-3.4.1.tar.gz /opt ; cd /opt
&] sudo tar -zxf setup-3.4.1.tar.gz ; cd setup-3.4.1 ; sudo chmod -R +x *

The OBDA (Open Bio Database Access) to obtain database entries, copy a sample configuration file in the BioRuby distribution
&] sudo cp bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini /etc/bioinformatics/seqdatabase.ini
&] cp bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini ~/.bioinformatics/seqdatabase.ini

The expat library dependency for RAA:xmlparser.
In Debian-like:
&] sudo apt-get -y install libexpat1
From source:
&] sudo cp ~/Downloads/expat-2.0.1.tar.gz /opt ; cd /opt
&] sudo tar -zxf expat-2.0.1.tar.gz ; cd expat ; sudo chmod -R +x *

The RAA:xmlparser for faster parsing of the BLAST XML output format.
&] sudo cp ~/Downloads/xmlparser-0.6.8.tar.gz /opt ; cd /opt
&] sudo tar -zxf xmlparser-0.6.8.tar.gz ; cd xmlparser ; sudo chmod -R +x *
&] sudo ruby extconf.rb --with-expat-lib=/usr/lib
&] sudo make
&] sudo make site-install

The RAA:bdb for creating faster flatfile index using Berkley DB (see documentation) :

The RAA:rmagick version1 and version2 (available thru gem) for outputting png and jpeg images.

The RAA:rake (available thru gem) for testing, developing ChemRuby.

Installation of optional librairies

Accessing BioSQL database created by other Open Bio* libraries.

The RubyForge:ActiveRecord available via gem
The RubyForge:MySQL/Ruby
The RubyForge:postgres-pr available via gem
The RubyForge:ActiveRecord Oracle enhanced adapter available via gem

For BioRuby 1.2.1+ (note that ruby-oci8 can only work with ruby-dbi 0.2.2).

The RubyForge:Ruby/DBI and at least one driver from MySQL/Ruby, postgres-pr, or RubyForge:ruby-oci8 .
The driver from MySQL/Ruby
The driver from postgres-pr
The RubyForge:ruby-oci8 (install Oracle or Oracle client first)

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