bmpvieira/afra repository overview
#Afra 
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 <[[email protected]]>(mailto:[email protected]) @yeban
Bruno Vieira <[email protected]> @bmpvieira
Yannick Wurm (yannick.poulet.org) @yannick__
License
Afra is licensed under the Apache 2.0 license.
Tag summary
Content type
Image
Digest
sha256:502bef442…
Size
503.4 MB
Last updated
almost 11 years ago
docker pull bmpvieira/afra