cbioportal-deployment

This package contains ansible plays for deploying a cBioPortal instance on a remote server.

The repository also contains an import play which can be used to add new data to the portal automatically.

Inventories

To make managing multiple sites possible, a range of deployments can be managed under a single directory, inventories. Each is a directory containing a hosts.ini file and a group_vars directory containing the settings needed for each group. All roles and deployments share settings.

Security

The group_vars files are encrypted using ansible-vault, so data in these files can be committed. The vault password is kept in a separate file, .vault-password, and configured so that it is read automatically when needed (using ansible.cfg). Obviously, .vault-password should never be committed to version control. It doesn't even need to exist, and can be given manually by prompt if needed.

To encrypt and decrypt these files, use a command like:

$ ansible-vault decrypt inventories/oicr/group_vars/all
$ ansible-vault encrypt inventories/oicr/group_vars/all

This makes maintenance a little clunkier than managing everything locally, but does provide a backup for all the settings. And nothing should be directly accessible anyway, as ssh keys are there to secure connections to the servers.

With virtualbox

This is demonstrated by inventories/virtualbox/hosts.ini.

These groups use a config like this from .ssh/config. I assume you have an ssh key set up accordingly.

Host virtualbox
  RSAAuthentication yes
  HostName 127.0.0.1
  IdentityFile ~/.ssh/virtualbox_rsa
  User root
  Port 2228

The command is then:

$ ansible-playbook -i inventories/virtualbox/hosts.ini provisioning.yml

Importing data

You can also use this project to manage importing, using the playbook import.yml.

The command is:

$ ansible-playbook -v -i inventories/virtualbox/hosts.ini --extra-vars="import_directory=..." import.yml