Pre-Requisites
A working setup of openCGA is required to setup a Testing environment. If user hasn't yet set it up, please follow the steps on installation guide and set it up.
Download Test Data
In order to populate the environment with real life data, Please download the test data from the following links :
Initialisation Scripts
Download the initialisation.sh script. All of the following steps assume, user is under openCGA installation directory (/opt/opencga/). Below you can find explanation of initialisation script step by step:
This CLI command will create the database, the collections and all the indexes, it also creates the admin user with the specified password. The MongoDB database host and name are read from the /conf/catalog-configuration.yml file by default.
./bin/opencga-admin.sh catalog install -p
This following command will create a user name "John Doe" and ID "test". Note that as by default OpenCGA is configured as private which means that only admin user can create other users. We are using opencga-admin CLI
./bin/opencga-admin.sh users create -p -u test --user-email test@gel.ac.uk --user-name "John Doe" --user-password
Now we will use this newly created user "test" for further actions, for this first user need to login. The next statement will do that:
./bin/opencga.sh users login -u test -p
This will create a hidden directory in your home called .opencga. This directory will contain a file named ~/.opencga/session.json with the users and the session id, this will be used automatically by opencga.sh, this is valid only for some minutes, by doing this users do not have to write the password too many times.