BioRuby 2.0.0 RELEASE NOTES

A lot of changes have been made to the BioRuby 2.0.0 after the version 1.5.x is released. This document describes important and/or incompatible changes since the BioRuby 1.5.0 release.

For known problems, see KNOWN_ISSUES.rdoc.

Features moved to separete gems

Some features are moved to separate gems because of reducing complexity and/or to avoid external library dependency of BioRuby core.

BioRuby Shell is moved to “bio-shell”

BioRuby Shell is split to “bio-shell” gem.

Executable files are moved to “bio-executables”

To avoid unexpected loading of executable files by some Rails software, all executable commands are moved to “bio-executables” gem (except the “bioruby” command that is included in the above “bio-shell” gem).

Fast BLAST XML result parser by using Expat XML Parser is moved to “bio-blast-xmlparser”

Fast BLAST XML result parser by using Expat XML Parser is split to “bio-blast-xmlparser” gem, because of external C library dependency. Please install “bio-blast-xmlparser” gem if possible. If it is installed, BioRuby automatically use it.

Bio::PhyloXML is moved to “bioruby-phyloxml”

Bio::PhyloXML is split to “bioruby-phyloxml” gem.

NOTE: Please uninstall “bio-phyloxml” gem, that have been created as a preliminary trial of splitting a module in 2012 and have not been maintained after that.

Bio::SQL is moved to “bio-biosql”

Bio::SQL is split to “bio-biosql” gem.

New features and improvements

HTTPS is used to access NCBI web services

As you may know, NCBI announced that all HTTP resources will be switched to HTTPS on September 30, 2016. To follow the transition, all URLs for accessing NCBI E-utilities in BioRuby are changed to use HTTPS.

In BioRuby, the following classes/modules are affected.

In some rare cases (especially when building Ruby and/or OpenSSL by yourself from source code), Ruby does not include SSL/TLS support, or Ruby fails to detect SSL root certificates. In such cases, you may need to reinstall or upgrade Ruby, OpenSSL (or alternatives), and/or SSL root certificates with appropriate configuration options. Alternatively, installing binary packages is generally a good idea.

KEGG::GENES#diseases and related methods are added

The following methods are added to KEGG::GENES, contributed by @kojix2.

Pre-calculated ambiguity codon tables in Bio::CodonTable

Pre-calculated ambiguity codon tables are added, contributed by Tomoaki NISHIYAMA.

Bug fixes

Incompatible changes

Bio::Taxonomy is removed and merged to Bio::PhyloXML::Taxonomy

Bio::Taxonomy in lib/bio/db/phyloxml/phyloxml_elements.rb was written for PhyloXML in 2009. It was intended to become general taxonomy data class in BioRuby in these days. However, no efforts have been made to improve the Bio::Taxonomy class, and it still remains to be a PhyloXML specific class. Because Bio::PhyloXML is split as a different Gem (Biogem) package, we now decide to remove Bio::Taxonomy and merge it to Bio::PhyloXML::Taxonomy.

In the codes using Bio::Taxonomy directly, changing Bio::Taxonomy to Bio::PhyloXML::Taxonomy or adding the following monkey patch may be needed.

module Bio
   unless defined? Taxonomy
      Taxonomy = Bio::PhyloXML::Taxonomy
   end
end

In the future, Bio::Taxonomy might be added as general taxonomy data class. The new Bio::Taxonomy might be incompatible with the current Bio::Taxonmy.

Some features are moved to separete gems

Some features are split to separete gems and removed from this “bio” gem. See the above “Features moved to separete gems” topics for details.

Known issues

The following issues are added or updated. See KNOWN_ISSUES.rdoc for other already known issues.

Other important news

Ruby 1.8 is no longer supported

Ruby 1.8.x is no longer supported. Though unsupported, some components may still run on Ruby 1.8.7. Please use Ruby 1.8.7 at your own risk with this version of BioRuby.

Installation without RubyGems is no longer supported

Installation by using setup.rb without RubyGems is no longer supported, and setup.rb is no longer included in BioRuby distribution.