bhanditz / seabase

Transcriptomic repository for multiple species

SeaBase

SeaBase is a tool for searching, analysing and sharing gene expression data of marine organisms.

Install

General requirements:

• Ruby version 2.3
• MySQL server version 5.7
• Web Server for production (Nginx, or Apache)

required packatges on Ubuntu:

sudo apt-get update
sudo apt-get install mysql-server csh libqt4-dev

Running in production with docker-compose

Get source code and switch to production branch

git clone https://github.com/GlobalNamesArchitecture/gnrd.git
cd gnrd
git checkout production

Create directories for database and configuration files

sudo mkdir -p /opt/seabase/data/mysql
sudo chown 999:999 -R /opt/seabase/data/mysql
sudo cp ./config/seabase-dev.env ./config/seabase-production.env

Modify seabase-production.env to suit your needs. Run compose in daemon mode from the project's root directory

nohup docker-compose up -d

Running Tests

Javascript tests use capybara-webkit, which requires installation of QT Webkit library, you can find installations instruction on capybara-webkit wiki

bundle exec rake db:migrate SEABASE_ENV=test
bundle exec rake db:seed SEABASE_ENV=test
bundle exec rake

Also look at .travis.yml file for more information

Running Tests With Docker Compose

Docker and Docker Compose need to be installed on the host machine

sudo rm -rf .sass-cache
docker-compose build
docker-compose up -d
docker-compose run app db:reset
docker-compose run app db:seed SEABASE_ENV=test
docker exec -it seabase_app_1 rake

For some reason docker-compose run app rake does not work for webkit-based tests.

Copyright

Code: Nathan Wilson,Dmitry Mozzherin

Copyright (c) 2014 Marine Biological Laboratory. See LICENSE for further details.