See java.com or reference your OS's installation instructions.

On Debian:

    $ sudo apt-get install littler r-cran-cairodevice

On Fedora:

    $ sudo yum install R-core

    $ rvm install 1.9.3
    $ rvm use 1.9.3

    $ gem install bundler
    $ bundle install

1. create a logs directory:mkdir logs
2. Use the included shotgun_server script to launch a development webserver at http:https://localhost:4567

    $ bin/shotgun_server

The server is a rack compatable application. Please consult the official guides for your webserver.

• Phusion Passenger Nginx Guide
• Phusion Passenger Apache Guide

Pull requests are welcome.

This is a sinatra app. Start by looking at lib/server.rb

• lib/server.rb - Where all the url controller methods live, along with the building of the commandline options for the plaac.jar

• views/*.haml - All the webpage templates. See haml docs for more info.

• views/js/*.coffee - All the javascript behavior, written in coffeescript.

Designed to handle the submission of FASTA files to a sequence analysis application called plaac

flow

  get '/' - input form and options
  post '/find' - runs plaac.jar
  get '/candidates/:token' - lists candidates, visualization input form
  post '/visualize' - runs plaac.jar for details and rscripts to visualize
  get '/visualize/:token' - visualization output
  
  # Downloadable content
  get '/candidates/:token/tsv' 
  get '/visualize/:token/pdf'
  get '/visualize/:token/images/:id.png' do
  get '/visualize/:token/tsv' do

  get '/details' - algorithm description and links.