Afra

TODO:
* Check if Omniauth works without proxy.
* Angular:
  * nav should be a directive
  * resolve.user should be a service
* Rewrite User & Session class using Sequel (migrations and model)
* For TTL, see: http://www.postgresql.org/message-id/689D39ED76CF4967B823E2718CF15A82@ticketevolution.com
* Keep database.rb? Probably not.
* Spec user model.
* Refactor Web & SessionManager class.
* Remove requirejs shims with jspm.io
* rake test:spec - run all specs
* rake - run all tests (alias to test:spec for now)
* If time permits, expose Google+ & Twitter login URL.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Integrate JBrowse.

Included JBrowse as git submodule, tracked from gh/yeban/jbrowse/afra.

Included for testing:
* MAKER2 generated gene prediction in GFF3 format for two scaffolds of fire ant
  genome.
* Gene prediction for the two scaffolds of fire ant genome in JB/JSON format.

If you `rackup -I lib`, then visit localhost:9292/#/genome, you will see a
working instance of JBrowse with a navbar on top.

NOTES

  * JB and supporting Dojo libraries have been symlinked from jbrowse/src into
    app/src/vendor.
  * All CSS dependencies of JBrowse have been compiled into one jbrowse.css
    file, with modifications to import directives to load necessary CSS from
    app/src/vendor.
  * All images from jbrowse/img have been copied to app/img.
  * JB's data is served from app/data/jb.

TODO
* Improve /genome.
  * JB shouldn't set page title.
  * Remove 'Full View' link.
  * Improve styling of tracks.
  * If possible, use fonts-awesome instead of JB's icon set.
* Rewrite JB's Perl scripts in Ruby (ev -> jb).
  * contents of data/jb should not be a part of the repository
* Task model
  * Sequel migrations for tasks table.
  * Task model
  * Script to populate tasks table from ev (ev -> pg)
* /jbrowse
  * Get the location of a task's JSON from server and call new Viewer() with
    it.  new Viewer() will require and initialize JB.
  * Next button at the bottom.  Clicking Next redoes the step above.
* Include a BAM file (and data in all formats supported by JB?) for
  testing.

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>