Genetic changes we can believe in: a web based tool for variant visualization and analysis
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README.markdown

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

Running

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.

Development

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.

Build javascript

Leiningen 2 required to build Clojure components. To compile JavaScript from ClojureScript source, watching for changes and automatically recompiling:

lein with-profile cljs cljsbuild auto

Starting the server

During development:

lein ring server-headless

License

Funding provided by the Harvard School of Public Health and EdgeBio; development by Keming Labs.

The code is freely available under the MIT license.

Copyright (c) 2012 Keming Labs, LLC