Gemfile

source 'http://rubygems.org'

gem 'rails', '3.2.2'

gem 'sqlite3'

#gem 'activeadmin'

gem 'json'

# Gems used only for assets and not required
# in production environments by default.
group :assets do
  gem 'sass-rails'
  gem 'uglifier'
end

group :development do
  gem 'rails-erd'
end

gem 'jquery-rails'

# Use unicorn as the web server
gem 'unicorn'

# Deploy with Capistrano
# gem 'capistrano'

# To use debugger
# gem 'ruby-debug'

gem 'execjs'
gem 'therubyracer'

gem 'sorcery' # access control

gem 'formtastic' # better forms

gem 'rjb' # ruby java bridge

gem 'thin' # better webserver than webrick

gem 'delayed_job' # queueing 

gem 'pry' # nicer rails console

gem 'rsruby' # R interface

gem 'spreadsheet' # xls file output

gem 'zip' # required by roo

gem 'nokogiri', '1.5.0' # nokogiri is required by roo but 1.5.2 broke google docs import 
gem 'roo' # google docs import

gem 'haml' # some widgets are in haml

gem 'bio' # for genbank and fasta export

gem 'xml-simple'