How to start the National Galaxy Server
- Become part of NBIC Galaxy group on SURFsara HPC cloud (sombrerogalaxy) so that you can log into https://ui.hpccloud.surfsara.nl/. Please contact Leon Mei or Rob Hooft for an account.
- Understand how to use HPC cloud (https://doc.hpccloud.surfsara.nl/)
- Has basic knowledge on Galaxy
- Has basic knowledge with git, docker and Ansible.
- Clone https://github.com/LUMC/galaxy-docker-ansible and go through the documentations
- TODO: We might need to have a different protected branch with versioned settings specific to the National Galaxy server.
How to start a new NBIC Galaxy
- Start a new VM with enough disk space. The best practice is to have an OS image (e.g., 30GB "NBIC-Galaxy-OS_ubuntu16.04_30GB") and a separate CEPH data image (e.g., 5TB "userdata_somb"). Make sure the VM name is "galaxy". Both OS and data images using for Galaxy are in persistent state, so all changes should be automatically saved.
- Once the VM is up and running, run the ansible playbook by following the instructions at galaxy-docker-ansible.
- the new VM will be "remote host" and HOSTNAME could be sombrerogalaxy.
- All the configuration values need to be set properly in the setting files located at host_vars/HOSTNAME.
How to update NBIC Galaxy
- Run the ansible playbook by following the instructions at galaxy-docker-ansible for update.