Installing BioRuby on Mac OS X

Disclaimer/Legal Stuff: Although it is unlikely that this procedure will cause the hard-drive or the OS to go completely haywire, I am not responsible if your system goes haywire(backing up is always a GOOD THING!)

I am also not at all an expert in Bioinformatics, so I don’t have the knowledge to help on any questions like “How do I do such and such with BioRuby”. I might be able to say what the Ruby code inside BioRuby does–syntax, as in “this method takes a block that does such and such” (but not the semantics–as in “this will find the patterns in DNA strands that are special in some way”).

  1. First, update the Ruby distribution on your Mac by following the instructions at Hivelogic.(Change the version numbers appropriately. I think the article says 1.8.4 etc, but the current version is at least 1.8.5
  2. Download the latest .gz source archive from BioRuby.
  3. Extract and find the README file. Read through it Here are the important parts I used(I did not use RubyGems).
  4. If your operating system supports ‘sudo’ command (such as Mac OS X),
    try the following procedure instead of the above. % ruby install.rb config
    % ruby install.rb setup
    % sudo ruby install.rb install

    You can run tests by

    % ruby install.rb test

    and run

    % ruby install.rb –help

  5. Start irb and try: require 'bio'
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