Bio

Bio is an Elixir package for developing bioinformatics software. It is greatly inspired by, if not based on, the bio-ruby gem (see http://bioruby.org/)

Installation

If available in Hex, the package can be installed as:

1. Add bio to your list of dependencies in mix.exs:

   def deps do [{:bio, "~> 0.0.1"}] end

2. Ensure bio is started before your application:

   def application do [applications: [:bio]] end

Ensembl Database

This package is currently set up to expect to connect to a MySQL database containing a copy of the Ensembl gene data (see http://www.ensembl.org). Currently being tested with the GRCH37 version, the default config looks for a database named homo_sapiens_core_75_37

Place this config in your config/config.exs file (or, if you're using Phoenix, the config file for the appropriate environment).

config :bio, Bio.Repo,
  adapter: Ecto.Adapters.MySQL,
  username: "",
  password: "",
  database: "homo_sapiens_core_75_37",
  hostname: "localhost",
  pool_size: 10

The tests are expecting to be able to connect to this database (and this version in particular) to ensure that the schemas are working properly.

Testing

The Gemfile(.lock) files and Guardfile at the root are there simply for testing. If you have the ruby gem Bundler installed, you can run:

bundle install
bundle exec guard

This will monitor the lib and test directories and rerun the appropriate tests when the source files change.