o8: genetic changes we can believe in
o8 handles the hard work of organizing and visualizing genetic variants, providing a web-based platform to interactively explore and analyze human variation data. It easily interoperates with analysis frameworks like Galaxy and GenomeSpace to supplement existing tools with a reactive, intuitive way to identify biologically relevant changes.
o8 is easy to setup and run on your own infrastructure, and a demonstration server is available to explore the system capabilities. It is an open source, freely available platform built on top of existing software:
- GATK: The Genome Analysis Toolkit from the Broad Institute
- gemini: a framework for mining genome variation, from the Quinlan lab
- snpEff: predicts functional consequences of variants, from McGill University
- bcbio.variation: a toolkit to compare and consolidate variation calls from multiple sources, developed at Harvard School of Public Health
The only required pieces of software are Java and the leiningen build tool. To run the server:
$ lein run -c config/web-processing.yaml
and your site will be available at 'http://localhost:8080`.
To enable functional annotation and querying of biological metrics, install gemini on the system as well.
Build HTML and CSS
Setup bundler (rubygem management gem) and use it to get other Ruby dependencies:
gem install bundler bundle install
To build from haml and sass:
bundle exec guard
to start the Guard watcher (use Chrome Livereload plugin for auto browser refresh). Hit return to build the HTML and CSS the first time.
lein with-profile cljs cljsbuild auto
Starting the server
lein ring server-headless
The code is freely available under the MIT license.
Copyright (c) 2012 Keming Labs, LLC