igv-rails

Installation

Add this line to the application's Gemfile:

gem 'igv-rails'

And then execute:

$ bundle

Or install it yourself as:

$ gem install igv-rails

Usage

Add IGV (and dependencies) to the application's Gemfile:

gem 'font-awesome-rails'
gem 'jquery-rails'
gem 'jquery-ui-rails'
gem 'igv-rails'

Require IGV (and dependencies) to the application's application.js:

//= require jquery
//= require jquery-ui
//= require igv

Require IGV CSS (and dependencies) to the application's application.css:

/*
*= require font-awesome
*= require jquery-ui
*= require igv
*/

Example

Provide a div container within a view:

<div id="myDiv"></div>

Provide javascript to configure and load IGV within the view:

$(document).ready(function () {
var div = $("#myDiv")[0],
options = {
    showNavigation: true,
    genome: "hg19",
    locus: "chr1:155,172,193-155,172,564",
    tracks: [
        {
            url: '//www.broadinstitute.org/igvdata/1KG/b37/data/NA06984/alignment/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20120522.bam',
            label: 'NA06984'
        }
    ]
};

igv.createBrowser(div, options);
});

Contributing

1. Fork it ( https://github.com/[my-github-username]/igv-rails/fork )
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request

Build Notes

This is igv-web GEMified for the Rails >= 4.1 asset pipeline through the following:

	bundle gem igv-rails
	cd igv-rails
	mkdir -p vendor/assets/javascripts
	curl http://igv.org/web/test/dist/igv.js -o vendor/assets/javascripts/igv.js
	mkdir -p vendor/assets/stylesheets
	curl http://igv.org/web/test/dist/css/igv.css -o vendor/assets/stylesheets/igv.css
	echo "" >> README.md; echo "# igv appended README #" >> README.md; echo "" >> README.md
	curl https://github.com/broadinstitute/igv-web/blob/master/README.md >> README.md
	echo "" >> LICENSE; echo "# igv appended LICENSE #" >> LICENSE; echo "" >> LICENSE
	curl https://github.com/broadinstitute/igv-web/blob/master/license.txt >> LICENSE
	git add .
	git commit -am "igv-rails"
	git remote add origin [email protected]:vanetten/igv-rails.git

• modify lib/igv/rails/version.rb to match igv-all.js version

    VERSION = "1.0.9.*"
  

• modify lib/igv/rails.rb to subclass Rails::Engine

    class Engine < ::Rails::Engine
    end
  

• modify igv-rails.gemspec

    spec.summary       = "IGV for Rails."
    spec.description   = "This gem provides igv javascript, css, and images for your Rails application."
    spec.homepage      = "https://github.com/vanetten/igv-rails"
    spec.files         = `git ls-files -z`.split("\x0") + ["LICENSE", "README.md"]
    spec.add_dependency "railties", "~> 4.1"
  

• build

    rake build
  

• release

    rake release
  

igv appended README

igv-web

Lightweight HTML-5 versison of the Integrative Genomics Viewer (http://www.broadinstitute.org/igv).