Please require your code below, respecting the bioruby directory tree. For instance, perhaps the only uncommented line in this file might be something like this:

require 'bio/sequence/awesome_sequence_plugin_thingy'

and then create the ruby file ‘lib/bio/sequence/awesome_sequence_thingy.rb’ and put your plugin’s code there. It is bad practice to write other code directly into this file, because doing so causes confusion if this biogem was ever to get merged into the main bioruby tree.