Genome Annotation for the Masses
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.extlib
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.ruby-version
ArrayRepr.pm
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ExternalSorter.pm
FastaDatabase.pm
FeatureTrack.pm
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GenomeDB.pm
IntervalStore.pm
JBlibs.pm
JsonFileStorage.pm
LICENSE.txt
LazyNCList.pm
LazyPatricia.pm
Makefile.PL
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NOTICE.txt
NameHandler.pm
README.md
Rakefile
Vcf.pm
app.rb
bower.json
package.json

README.md

Afra Build Status

Crowdsourcing platform for gene annotation

Run using Docker image from registry

docker run -i -t -p 9292:9292 bmpvieira/afra

Run using Docker image locally built

docker build -t afra .
docker run -i -t -p 9292:9292 afra

Install and Run without Docker

Ruby 2.0

ruby-install, chruby and chgems is prescribed so as to facilitate troubleshooting potential issue with Ruby setup. You can use rbenv, etc. as well.

Ruby 2.x ships with RubyGems 2.x and Rake 10.x which are required to setup and run Afra. If you install Ruby from your package manager, you may have to install RubyGems and Rake separately.

# install ruby-install (https://github.com/postmodern/ruby-install).
$ cd
$ wget -O ruby-install-0.3.0.tar.gz https://github.com/postmodern/ruby-install/archive/v0.3.0.tar.gz
$ tar xvf ruby-install-0.3.0.tar.gz
$ cd ruby-install-0.3.0/
$ sudo make install

# install Ruby 2.0
$ sudo ruby-install ruby

# install chruby (https://github.com/postmodern/chruby)
$ cd
$ wget -O chruby-0.3.7.tar.gz https://github.com/postmodern/chruby/archive/v0.3.7.tar.gz
$ tar xvf chruby-0.3.7.tar.gz
$ cd chruby-0.3.7/
$ sudo make install

# install chgems (https://github.com/postmodern/chgems)
$ cd
$ wget -O chgems-0.3.2.tar.gz https://github.com/postmodern/chgems/archive/v0.3.2.tar.gz
$ tar xvf chgems-0.3.2.tar.gz
$ cd chgems-0.3.2/
$ sudo make install

Perl 5

Should be pre-installed on your system.

Node 0.11.11

n is prescribed to facilitate troubleshooting possible issues with Node setup. You can use nvm, etc.

Recent releases of Node ships with npm which is required to setup and run Afra. If you install Node from your package manager, you may have to install npm separately.

$ wget -c https://github.com/visionmedia/n/archive/1.2.1.tar.gz
$ tar xvf 1.2.1.tar.gz
$ cd n-1.2.1
$ sudo make install
$ sudo n latest

Postgres 9.3

Mac

$ brew install postgresql

You may have to separately install libpqxx.

$ brew install libpqxx

Then,

$ createdb `whoami`

Linux (Debian)

$ sudo aptitude install postgresql-9.3
$ sudo -u postgres createuser --interactive # when asked, make role superuser
$ sudo -u postgres createdb <name of the role used in previous step>

Afra

$ git clone https://github.com/yeban/afra.git
$ cd afra
$ rake
$ ruby -r ./app.rb -e 'App.migrate'
$ ruby -r ./app.rb -e 'App.gff2jbrowse'
$ ruby -r ./app.rb -e 'App.register_features'
$ ruby -r ./app.rb -e 'App.create_tasks'

Copy env.yml.example and set facebook_app_id and facebook_app_secret and session_secret (this can be any string).

$ ruby -r ./app.rb -e 'App.serve'

Contacts

Anurag Priyam <[anurag08priyam@gmail.com]>(mailto:anurag08priyam@gmail.com) @yeban
Bruno Vieira <mail@bmpvieira.com> @bmpvieira
Yannick Wurm (yannick.poulet.org) @yannick__

License

Afra is licensed under the Apache 2.0 license.

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