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1 README.rdoc - README for BioRuby
2 Copyright:: Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org>,
3 2008 Jan Aerts <jandot@bioruby.org>
4 License:: The Ruby License
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5
6 = BioRuby
7
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8 BioRuby is an open source Ruby library for developing bioinformatics
9 software. Object oriented scripting language Ruby has many features
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10 suitable for bioinformatics research, for example, clear syntax to
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11 express complex objects, regular expressions for text handling as
12 powerful as Perl's, a wide variety of libraries including web service
13 etc. As the syntax of the Ruby language is simple and very clean, we
14 believe that it is easy to learn for beginners, easy to use for
15 biologists, and also powerful enough for the software developers.
16
17 In BioRuby, you can retrieve biological database entries from flat
18 files, internet web servers and local relational databases. These
19 database entries can be parsed to extract information you need.
20 Biological sequences can be treated with the fulfilling methods of the
21 Ruby's String class and with regular expressions. Daily tools like
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22 Blast, Fasta, Hmmer and many other software packages for biological
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23 analysis can be executed within the BioRuby script, and the results
24 can be fully parsed to extract the portion you need. BioRuby supports
25 major biological database formats and provides many ways for accessing
26 them through flatfile indexing, SQL, web services etc. Various web
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27 services including KEGG API can be easily utilized by BioRuby.
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28
29
30 == FOR MORE INFORMATION
31
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32 BioRuby's official website is at http://bioruby.org/.
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33 You will find links to related resources including downloads,
34 mailing lists, Wiki documentation etc. in the top page.
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35
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36 * http://bioruby.org/
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37
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38
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39 == WHERE TO OBTAIN
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40
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41 === WWW
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42
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43 The stable release is freely available from the BioRuby website.
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44
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45 * http://bioruby.org/archive/
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46
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47 === git
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48
49 If you need the latest development version, this is provided at
50
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51 * http://github.com/bioruby/bioruby
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52
53 and can be obtained by the following procedure:
54
55 % git clone git://github.com/bioruby/bioruby.git
56
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57 ==== CVS
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58
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59 CVS is now deprecated as source control has moved to github. Please use git
60 instead of CVS. For historical purposes: the anonymous CVS was provided at
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61
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62 * http://cvs.bioruby.org/
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63
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64 and could be obtained by the following procedure.
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65
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66 % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby login
67 CVS password: cvs (login with a password 'cvs' for the first time)
68 % cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioruby co bioruby
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69
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70 === RubyGems
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71
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72 RubyGems[URL:http://rubyforge.org/projects/rubygems/] version of
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73 the BioRuby package is also available for easy installation.
74
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75 * http://rubyforge.org/projects/bioruby/
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76
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77
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78 == REQUIREMENTS
79
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80 * Ruby 1.8.2 or later -- http://www.ruby-lang.org/
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81 (Ruby 1.8.5 or later is recommended)
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82
83 == OPTIONAL REQUIREMENTS
84
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85 Some optional libraries can be utilized to extend BioRuby's functionality.
86 If your needs meets the following conditions, install them from the "Ruby
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87 Application Archive" at http://raa.ruby-lang.org/, RubyForge at
88 http://rubyforge.org/, or the following web sites.
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89
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90 For faster parsing of the BLAST XML output format:
91
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92 * {RAA:xmlparser}[http://raa.ruby-lang.org/project/xmlparser/]
3b5e549 @ktym * notes on ruby 1.8.0
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93
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94 Creating faster flatfile index using Berkley DB:
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95
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96 * {RAA:bdb}[http://raa.ruby-lang.org/project/bdb/]
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97
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98 Accessing BioSQL database created by other Open Bio* libraries:
99
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100 * {RubyForge:ActiveRecord}[http://rubyforge.org/projects/activerecord/]
101 and at least one driver (or adapter) from
102 {RubyForge:MySQL/Ruby}[http://rubyforge.org/projects/mysql-ruby/],
103 {RubyForge:postgres-pr}[http://rubyforge.org/projects/postgres-pr], or
104 {RubyForge:ActiveRecord Oracle enhanced adapter}[http://rubyforge.org/projects/oracle-enhanced/].
105 * For BioRuby 1.2.1 or older version,
106 {RubyForge:Ruby/DBI}[http://rubyforge.org/projects/ruby-dbi] and
107 at least one driver from MySQL/Ruby, postgres-pr, or
108 {RubyForge:ruby-oci8}[http://ruby-oci8.rubyforge.org/]
109 (note that ruby-oci8 can only work with ruby-dbi 0.2.2).
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110
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111
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112 == INSTALL
113
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114 In the bioruby source directory (such as bioruby-x.x.x/), run setup.rb
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115 as follows:
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116
117 % su
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118 # ruby setup.rb
119
120 These simple step installs this program under the default location of
121 Ruby libraries. You can also install files into your favorite directory
122 by supplying setup.rb some options. Try "ruby setup.rb --help".
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123
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124 If your operating system supports 'sudo' command (such as Mac OS X),
125 try the following procedure instead of the above.
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126
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127 % sudo ruby setup.rb
128
129 For older version users: "install.rb" is now renamed to "setup.rb".
130 The options "config", "setup", and "install" are still available.
131
132 % ruby setup.rb config
133 % ruby setup.rb setup
134 % su
135 # ruby setup.rb install
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136
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137 You can run tests by
138
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139 % ruby setup.rb test
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140
141 and run
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142
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143 % ruby setup.rb --help
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144
145 for more details.
146
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147 === RubyGems
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148
149 If you are using RubyGems, just type
150
151 % gems install bio
152
153
154 == SETUP
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155
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156 If you want to use the OBDA (Open Bio Database Access) to obtain database
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157 entries, copy a sample configuration file in the BioRuby distribution
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158
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159 bioruby-x.x.x/etc/bioinformatics/seqdatabase.ini
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160
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161 to
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162
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163 /etc/bioinformatics/seqdatabase.ini (system wide configuration)
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164
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165 or
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166
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167 ~/.bioinformatics/seqdatabase.ini (personal configuration)
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168
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169 and change the contents according to your preference. For more
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170 information on the OBDA, see http://obda.open-bio.org/ .
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171
172
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173 == USAGE
174
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175 You can load all BioRuby classes just by requiring 'bio.rb'. All the
176 BioRuby classes and modules are located under the module name 'Bio' to
177 separate the name space.
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178
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179 #!/usr/bin/env ruby
180 require 'bio'
181
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182 You can also read other documentation in the 'doc' directory.
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183
184 bioruby-x.x.x/doc/
185
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186 === RubyGems
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187
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188 With RubyGems, you need to load 'rubygems' library before using 'bio'.
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189
190 #!/usr/bin/env ruby
191 require 'rubygems'
192 require_gem 'bio'
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193
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195 == LICENSE
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196
c5677d0 @ktym * BioRuby is now distributed under the same terms as Ruby
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197 BioRuby can be freely distributed under the same terms as Ruby.
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198
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199 Note that setup.rb included in the BioRuby package comes from
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200 {RAA:setup}[http://raa.ruby-lang.org/project/setup/] developed by Minero Aoki
201 (http://i.loveruby.net/en/projects/setup/).
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202
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203
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204 == CONTACT
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205
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206 Current staff of the BioRuby project can be reached by sending e-mail
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207 to <staff@bioruby.org>.
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208
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