sbliven / basespace-dojo Goto Github PK

This README would normally document whatever steps are necessary to get the application up and running.

In order to make this experimental Illumina BaseSpace’s application to run you need to follow these steps:

Ruby and Rails can be conveniently installed via the Ruby Version Manager (RVM):

\curl https://raw.github.com/wayneeseguin/rvm/master/binscripts/rvm-installer | bash -s stable --rails

On Mac OS X, Ruby comes preinstalled. However, for the development installation using RVM, it is necessary to install [MacPorts](www.macports.org/install.php) and then execute ‘sudo port install curl`.

Note: On both Linux and Mac OS X it is necessary to have superuser (“sudo”) permissions.

Train a Ninja to sneak into the Dojo

git clone https://github.com/helios/basespace-ninja
cd basespace-ninja
bundle install
rake gemspec

Setup the Dojo with the hidden Ninja inside

git clone https://github.com/helios/basespace-dojo
cd basespace-dojo
bundle install

Use the Ninja’ secrets for accessing BaseSapce, create a file name

credentials.json

with your credentialns

{
  "client_id":      "",
  "client_secret":  "",
  "app_session_id": "",
  "access_token":   "",
  "basespace_url":  "https://api.basespace.illumina.com/",
  "api_version":    "v1pre3"
}

Open the Dojo to the public

BASESPACE_CREDENTIALS=path_to_your_json_credentials_file rails s

Things you may want to cover:

• Ruby version

• System dependencies

• Configuration

• Database creation

• Database initialization

• How to run the test suite

• Services (job queues, cache servers, search engines, etc.)

• Deployment instructions

• …

Please feel free to use a different markup language if you do not plan to run rake doc:app.

BaseSpace Ruby SDK is not deployed as a gem yet. The development version can be installed using bundler like Dojo and Ninja above, but that does not work on all systems. The sure-fire way of instally BaseSpace Ruby SDK is:

git clone https://github.com/joejimbo/basespace-ruby-sdk.git
cd basespace-ruby-sdk
rake gemspec
gem build bio-basespace-sdk.gemspec
gem install bio-basespace-sdk-0.1.2.gem