pasted / clinical_variant_database

Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensembl dataset. Originally developed as part of a Masters in Bioinformatics project @ University of Exeter

#Clinical Variant Database Rails application for storing and parsing clinical VCF files. Gene annotations can be retrieved via Biomart integration from Ensembl dataset.

##Features

• VCF file upload and parsing.
• Serialised storage of hashed values into postgreSQL Hstore field - allows NoSQL-type unstructured data to be stored within an overall relational database structure (ACID-compliant key/value stores).
• Integration with Biomart (hsapiens_gene_ensembl, omim), other datasets can also be interrogated.
• Integration with Provean (Protein Variation Effect Analyzer) via Mechanize
• Pagination,Search and sorting functionality for Variants, using Ransack and Kaminari.
• Batch update of Gene/Disorder annotation using Sidekick / redis workers.
• Relationships between Samples to reflect parent-offspring by Closure trees.

##Installation

Requires:

• PostgreSQL
• Redis
• Ruby 1.9.2 or newer
• Rails 3.2

Clone the repository to your web server's public directory, initiallizing Git if required;

	git init
	git clone https://github.com/pasted/clinical_variant_database.git

The config/database.yml file is not included in the repository, the template is included below(along with the increased number of database connections for use with Sidekiq / Redis). Modify to include your database username and password, then save in the config directory.

development:
  adapter: postgresql
  encoding: utf8
  reconnect: false
  database: cvd_development
  pool: 25
  username: 
  password: 
  host: localhost

# Warning: The database defined as "test" will be erased and
# re-generated from your development database when you run "rake".
# Do not set this db to the same as development or production.
test:
  adapter: postgresql
  encoding: utf8
  reconnect: false
  database: cvd_test
  pool: 25
  username: 
  password: 
  host: localhost

production:
  adapter: postgresql
  encoding: utf8
  reconnect: false
  database: cvd_production
  pool: 25
  username: 
  password: 
  host: localhost

Then run the following commands in the app directory;

	bundle install
	rake db:create
	rake db:migrate
	rake db:seed

To start the application, first start up Redis by typing the following in the directory that you have installed redis.

	redis-server redis.conf

Then start Sidekiq in the application directory

 	 bundle exec sidekiq

More information on Sidekiq can be found on it's homepage. Finally if not using another webserver, such as Apache - start Rails webrick server (in the application directory)

	rails s