README.rdoc in bio-1.4.3.0001 vs README.rdoc in bio-1.5.0

- old
+ new

@@ -1,10 +1,10 @@ -- = README.rdoc - README for BioRuby Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>, Copyright (C) 2008 Jan Aerts <jandot@bioruby.org> - Copyright (C) 2011-2012 Naohisa Goto <ng@bioruby.org> + Copyright (C) 2011-2015 Naohisa Goto <ng@bioruby.org> License:: The Ruby License * The above statement is limited to this file. See below about BioRuby's copyright and license. ++ @@ -29,11 +29,11 @@ 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. +services can be easily utilized by BioRuby. == FOR MORE INFORMATION See RELEASE_NOTES.rdoc for news and important changes in this version. @@ -43,34 +43,34 @@ ==== 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-1.4.3.rdoc:: News and incompatible changes from 1.4.2 to 1.4.3. 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-1.4.3:: changes from 1.4.2 to 1.4.3. 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. @@ -97,50 +97,49 @@ === RubyGems {RubyGems (packaging system for Ruby)}[http://rubygems.org/] version of the BioRuby package is also available for easy installation. -* http://rubyforge.org/projects/bioruby/ +* https://rubygems.org/gems/bio === git If you need the latest development version, this is provided at -* http://github.com/bioruby/bioruby +* https://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) -- http://www.ruby-lang.org/ - * Ruby 1.9.3-p194 or later, or Ruby 1.8.7-p358 or later is recommended. +* Ruby 1.8.7 or later (except Ruby 1.9.0) -- http://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. == 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 -http://raa.ruby-lang.org/, RubyForge at http://rubyforge.org/, GitHub at -http://github.com/, or the following web sites. +or download and install from the following web sites. For faster parsing of the BLAST XML output format: -* {RAA:xmlparser}[http://raa.ruby-lang.org/project/xmlparser/] +* {xmlparser}[https://rubygems.org/gems/xmlparser] * For Ruby 1.8: {gem install xmlparser}[http://rubygems.org/gems/xmlparser] - * For Ruby 1.9: http://www.yoshidam.net/Ruby.html#xmlparser + * For Ruby 1.9 or later: http://www.yoshidam.net/Ruby.html#xmlparser * In both cases, {The Expat XML Parser}[http://expat.sourceforge.net/] and C compiler will be required. Creating faster flatfile index using Berkley DB: * {GitHub:ruby-bdb}[https://github.com/knu/ruby-bdb] - (which took over {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/]) + (which took over {bdb}[https://github.com/ruby-bdb/bdb]) (No RubyGems available) * {Oracle Berkeley DB}[http://www.oracle.com/technetwork/database/berkeleydb/index.html] and C compiler will be required. Accessing BioSQL database created by other Open Bio* libraries: @@ -157,26 +156,21 @@ * {gem install libxml-ruby}[http://rubygems.org/gems/libxml-ruby] * {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/] 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}[https://rubygems.org/gems/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 -http://rubyforge.org/projects/bioruby/ and install it by using gems command. +http://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 http://rubygems.org/ . === INSTALL without RubyGems @@ -301,12 +295,12 @@ 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}[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki -(http://i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1. +under different license. For example, setup.rb which comes from "setup" +developed by Minero Aoki (http://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