igv-rails 0.0.1.12

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in igv-rails.gemspec
+gemspec

data/LICENSE

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+
+# igv appended LICENSE #
+
+{"error":"Not Found"}

data/LICENSE.txt

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+Copyright (c) 2015 William Van Etten
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# igv-rails
+
+## Installation
+
+Add this line to the application's Gemfile:
+
+```ruby
+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:
+
+```ruby
+gem 'font-awesome-rails'
+gem 'jquery-rails'
+gem 'jquery-ui-rails'
+gem 'igv-rails'
+```
+
+Require IGV (and dependencies) to the application's application.js:
+
+```javascript
+//= require jquery
+//= require jquery-ui
+//= require igv-all
+```
+
+Require IGV CSS (and dependencies) to the application's application.css:
+
+```css
+/*
+*= require font-awesome
+*= require jquery-ui
+*= require igv
+*/
+```
+
+## Example
+
+Provide a div container within a view:
+
+```html
+<div id="myDiv"></div>
+```
+
+Provide javascript to configure and load IGV within the view:
+
+```javascript
+$(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](https://www.broadinstitute.org/software/igv/home) 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://www.broadinstitute.org/igv/projects/igv-web/dist/igv-all.min.js -o vendor/assets/javascripts/igv-all.js
+		mkdir -p vendor/assets/stylesheets
+		curl http://www.broadinstitute.org/igv/projects/igv-web/css/igv.css -o vendor/assets/stylesheets/igv.css
+		mkdir -p vendor/assets/images
+		curl http://www.broadinstitute.org/igv/projects/igv-web/dist/igv-all.min.map -o vendor/assets/images/igv-all.min.map
+		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 git@github.com:vanetten/igv-rails.git
+
+* modify **lib/igv/rails/version.rb** to match igv-all.js version
+
+		VERSION = "0.0.1.*"
+
+* 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).

data/Rakefile

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+require "bundler/gem_tasks"
+

data/igv-rails.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'igv/rails/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "igv-rails"
+  spec.version       = Igv::Rails::VERSION
+  spec.authors       = ["William Van Etten, PhD"]
+  spec.email         = ["vanetten@bioteam.net"]
+  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.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0") + ["LICENSE", "README.md"]
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency "railties", "~> 4.1"
+  spec.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+end

data/lib/igv/rails/version.rb

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+module Igv
+  module Rails
+    VERSION = "0.0.1.12"
+  end
+end

data/lib/igv/rails.rb

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+require "igv/rails/version"
+
+module Igv
+  module Rails
+	class Engine < ::Rails::Engine
+	end
+  end
+end