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:
-
Add bio to your list of dependencies in
mix.exs
:def deps do [{:bio, "~> 0.0.1"}] end
-
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.