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acd9e6d @ngoto Clarified copyright of README.rdoc and BioRuby
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1 --
2 = README.rdoc - README for BioRuby
3 Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
4 Copyright (C) 2008 Jan Aerts <jandot@bioruby.org>
5 License:: The Ruby License
6 * The above statement is limited to this file. See below about BioRuby's
7 copyright and license.
8 ++
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9
10 = BioRuby
11
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12 Copyright (C) 2001-2010 Toshiaki Katayama <k@bioruby.org>
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13
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14 BioRuby is an open source Ruby library for developing bioinformatics
15 software. Object oriented scripting language Ruby has many features
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16 suitable for bioinformatics research, for example, clear syntax to
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17 express complex objects, regular expressions for text handling as
18 powerful as Perl's, a wide variety of libraries including web service
19 etc. As the syntax of the Ruby language is simple and very clean, we
20 believe that it is easy to learn for beginners, easy to use for
21 biologists, and also powerful enough for the software developers.
22
23 In BioRuby, you can retrieve biological database entries from flat
24 files, internet web servers and local relational databases. These
25 database entries can be parsed to extract information you need.
26 Biological sequences can be treated with the fulfilling methods of the
27 Ruby's String class and with regular expressions. Daily tools like
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28 Blast, Fasta, Hmmer and many other software packages for biological
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29 analysis can be executed within the BioRuby script, and the results
30 can be fully parsed to extract the portion you need. BioRuby supports
31 major biological database formats and provides many ways for accessing
32 them through flatfile indexing, SQL, web services etc. Various web
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33 services including KEGG API can be easily utilized by BioRuby.
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34
35
36 == FOR MORE INFORMATION
37
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38 === Documents in this distribution
39
40 ==== General information
41
42 README.rdoc:: This file. General information and installation procedure.
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43 RELEASE_NOTES.rdoc:: News and important changes in this release.
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44 KNOWN_ISSUES.rdoc:: Known issues and bugs in BioRuby.
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45 doc/RELEASE_NOTES-1.4.0.rdoc:: News and incompatible changes from 1.3.1 to 1.4.0.
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46 doc/Changes-1.3.rdoc:: News and incompatible changes from 1.2.1 to 1.3.0.
47 doc/Changes-0.7.rd:: News and incompatible changes from 0.6.4 to 1.2.1.
48
49 ==== Tutorials and other useful information
50
51 doc/Tutorial.rd:: BioRuby Tutorial.
52 doc/Tutorial.rd.html:: HTML version of Tutorial.rd.
53 doc/KEGG_API.rd:: Documents about KEGG API, including usage of Bio::KEGG::API.
54
55 ==== BioRuby development
56
57 ChangeLog:: History of changes.
58 README_DEV.rdoc:: Describes ways to contribute to the BioRuby project, including coding styles and documentation guidelines.
59
60 ==== Documents written in Japanese
61
62 doc/Tutorial.rd.ja:: BioRuby Tutorial written in Japanese.
63 doc/Tutorial.rd.ja.html:: HTML version of Tutorial.rd.ja.
64 doc/KEGG_API.rd.ja:: Japanese translation of KEGG_API.rd.
65
66
67 === WWW
68
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69 BioRuby's official website is at http://bioruby.org/.
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70 You will find links to related resources including downloads,
71 mailing lists, Wiki documentation etc. in the top page.
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72
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73 * http://bioruby.org/
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74
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75
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76 == WHERE TO OBTAIN
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77
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78 === WWW
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79
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80 The stable release is freely available from the BioRuby website.
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81
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82 * http://bioruby.org/archive/
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83
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84 === RubyGems
85
86 RubyGems[URL:http://rubyforge.org/projects/rubygems/] version of
87 the BioRuby package is also available for easy installation.
88
89 * http://rubyforge.org/projects/bioruby/
90
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91 === git
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92
93 If you need the latest development version, this is provided at
94
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95 * http://github.com/bioruby/bioruby
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96
97 and can be obtained by the following procedure:
98
99 % git clone git://github.com/bioruby/bioruby.git
100
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101 ==== CVS
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102
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103 CVS is now deprecated as source control has moved to github. Please use git
104 instead of CVS. For historical purposes: the anonymous CVS was provided at
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105
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106 * http://cvs.bioruby.org/
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107
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108 and could be obtained by the following procedure.
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109
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110 % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
111 CVS password: cvs (login with a password 'cvs' for the first time)
112 % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby
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113
114
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115 == REQUIREMENTS
116
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117 * Ruby 1.8.2 or later (except Ruby 1.9.0) -- http://www.ruby-lang.org/
118 * Ruby 1.8.7-p174 or later, or Ruby 1.8.6-p383 or later is recommended.
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119 * Not yet fully ready with Ruby 1.9, although many components can now work
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120 in Ruby 1.9.1 and Ruby 1.9.2.
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121
122 == OPTIONAL REQUIREMENTS
123
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124 Some optional libraries can be utilized to extend BioRuby's functionality.
125 If your needs meets the following conditions, install them from the "Ruby
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126 Application Archive" at http://raa.ruby-lang.org/, RubyForge at
127 http://rubyforge.org/, or the following web sites.
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128
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129 For faster parsing of the BLAST XML output format:
130
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131 * {RAA:xmlparser}[http://raa.ruby-lang.org/project/xmlparser/]
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132
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133 Creating faster flatfile index using Berkley DB:
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134
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135 * {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/]
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136
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137 Accessing BioSQL database created by other Open Bio* libraries:
138
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139 * {RubyForge:ActiveRecord}[http://rubyforge.org/projects/activerecord/]
140 and at least one driver (or adapter) from
141 {RubyForge:MySQL/Ruby}[http://rubyforge.org/projects/mysql-ruby/],
142 {RubyForge:postgres-pr}[http://rubyforge.org/projects/postgres-pr], or
143 {RubyForge:ActiveRecord Oracle enhanced adapter}[http://rubyforge.org/projects/oracle-enhanced/].
144 * For BioRuby 1.2.1 or older version,
145 {RubyForge:Ruby/DBI}[http://rubyforge.org/projects/ruby-dbi] and
146 at least one driver from MySQL/Ruby, postgres-pr, or
147 {RubyForge:ruby-oci8}[http://ruby-oci8.rubyforge.org/]
148 (note that ruby-oci8 can only work with ruby-dbi 0.2.2).
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149
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150 For parsing PhyloXML format files:
151
152 * {RubyForge:libxml-ruby}[http://libxml.rubyforge.org/] (Ruby language
153 bindings for the {GNOME Libxml2 XML toolkit}[http://xmlsoft.org/])
a3441af @latvianlinuxgirl Newly added PhyloXML support written by Diana Jaunzeikare.
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154
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155
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156 == INSTALL
157
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158 In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb
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159 as follows:
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160
161 % su
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162 # ruby setup.rb
163
164 These simple step installs this program under the default location of
165 Ruby libraries. You can also install files into your favorite directory
166 by supplying setup.rb some options. Try "ruby setup.rb --help".
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167
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168 If your operating system supports 'sudo' command (such as Mac OS X),
169 try the following procedure instead of the above.
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170
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171 % sudo ruby setup.rb
172
173 For older version users: "install.rb" is now renamed to "setup.rb".
174 The options "config", "setup", and "install" are still available.
175
176 % ruby setup.rb config
177 % ruby setup.rb setup
178 % su
179 # ruby setup.rb install
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180
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181 You can run tests by
182
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183 % ruby setup.rb test
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184
185 and run
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186
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187 % ruby setup.rb --help
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188
189 for more details.
190
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191 === RubyGems
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192
193 If you are using RubyGems, just type
194
195 % gems install bio
196
197
198 == SETUP
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199
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200 If you want to use the OBDA (Open Bio Database Access) to obtain database
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201 entries, copy a sample configuration file in the BioRuby distribution
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202
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203 bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini
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204
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205 to
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206
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207 /etc/bioinformatics/seqdatabase.ini (system wide configuration)
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208
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209 or
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210
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211 ~/.bioinformatics/seqdatabase.ini (personal configuration)
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212
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213 and change the contents according to your preference. For more
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214 information on the OBDA, see http://obda.open-bio.org/ .
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215
216
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217 == USAGE
218
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219 You can load all BioRuby classes just by requiring 'bio.rb'. All the
220 BioRuby classes and modules are located under the module name 'Bio' to
221 separate the name space.
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222
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223 #!/usr/bin/env ruby
224 require 'bio'
225
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226 You can also read other documentation in the 'doc' directory.
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227
228 bioruby-x.x.x/doc/
229
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230 === RubyGems
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231
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232 With RubyGems, you need to load 'rubygems' library before using 'bio'.
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233
234 #!/usr/bin/env ruby
235 require 'rubygems'
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236 require 'bio'
237
238 With old version of RubyGems, use 'require_gem' which was deprecated in
239 RubyGems 0.9.0 and removed in RubyGems 1.0.1.
240
241 #!/usr/bin/env ruby
242 require 'rubygems'
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243 require_gem 'bio'
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244
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245
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246 == LICENSE
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247
c5677d0 @ktym * BioRuby is now distributed under the same terms as Ruby
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248 BioRuby can be freely distributed under the same terms as Ruby.
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249 See the file COPYING (or COPYING.ja written in Japanese).
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250
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251 As written in the file COPYING, see the file LEGAL for files distributed
252 under different license. For example, setup.rb which comes from
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253 {RAA:setup}[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki
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254 (http://i.loveruby.net/en/projects/setup/) is licensed under LGPL 2.1.
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255
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256
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257 == CONTACT
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258
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259 Current staff of the BioRuby project can be reached by sending e-mail
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260 to <staff@bioruby.org>.
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261
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