alternative instructions for getting app running

gistfile1.txt

$ biogem --with-engine Foo foo
$ cd bioruby-foo
$ rake version:write
update gemfile to specify new version of bundler
$ bundle install
Note: a database is automatically configure for the newly created gem
$ cd ../
$ rails new Webfoo
$ add `gem 'bio-foo', :path=>'path_gem_dir' `  into Rails application Gemfile the newly created gem:
$ cd Webfoo

$(maybe also: bundle exec rake gemspec, then update gem's gemspec file where marked TODO:)
$ bundle install


Enable the route for the added gem (in biouby-foo/config/routes.rb) uncomment:

yourPathToTheControllerFiles = "/"
controllerName = :foos
#otherControllerName = :samples
#---
scope mount_at, yourPathToTheControllerFiles do    
  resources controllerName do
    member do
      get :example
    end
  end
#  resources otherControllerName, :only =>[:index, :show]
end #scope


In bioruby-foo/lib/bio/foo/example.rb be sure the example class is uncommented:

module Bio
  module Foo
    class Example < DummyConn
    end
  end
end

in bioruby-foo find all instances of Foo in Foo_controller, folder and file names, views etc and change to name of gem 

uncomment contents of db/migrate/001_create_example.rb

cd bioruby-foo
bundle exec rake db:create
bundle exec rake db:migrate

@sbliven - alternative instructions

1. Change Gemfile to accept bundler >= 1.0.0 rather than ~> 1.0.0
2. bundle install before rake so it installs missing dependencies
3. Add gem install rails, or list as prereq
4. Need to add gem path to Gemfile before line 12
   gem 'bio-foo', :path=>'/full/path/to/bioruby-foo'
5. Add bundle exec rake gemspec before line 6, as well as instructions to remove TODO messages from gemspec
6. Note line 8: package 'bio-foo', but repository 'bioruby-foo'

Thanks I'll update docs and implementation