Create a host to test on

  1. go to the galaxy-launcher repository
  2. go to test/vagrant/ubuntu-16.04
  3. Type vagrant up
  4. go to the galaxy-launcher repository
  5. copy the hosts.sample file to host

Exercise: Set up your own hosts file. Use test/hosts as an example.

  1. Check if you can reach the host by ansible -m ping HOSTNAME (insert your own hostname here)

Create the settings files for your host.

  1. copy files/example_host to files/HOSTNAME
  2. copy host_vars/example_host to host_vars/HOSTNAME
  3. Uncomment the commented out variables in host_vars/HOSTNAME/galaxy_settings.yml and change them to your preferred settings.
  4. Use the guide on Björn Grünings page to add some settings to your galaxy that you like in galaxy_docker_optional_environment_settings.
  5. Change the version of the docker image to 17.09 or whatever version you like in host_vars/HOSTNAME/docker_settings.yml
  6. Install the prerequisites on your test vm by running ansible-playbook main.yml -e "host=HOSTNAME run=install_prerequisites".
  7. Install galaxy on your test VM by running ansible-playbook main.yml -e "host=HOSTNAME run=install_galaxy".
  8. Galaxy should now be accessible on localhost:8081

Provision your galaxy


Exercise: go to files/example_host/tool/tool_list.yaml.sample and use this as an example to create your own tool_list.yaml. Include at least one data manager tool.

Tools can be installed by running ansible-playbook main.yml -e "host=HOSTNAME run=install_tools".


Exercise: go to files/example_host/dbkeys/dbkeys.yaml.sample and use this as an example to create your own dbkeys.yaml.

Genomes can be installed by running ansible-playbook main.yml -e "host=HOSTNAME run=install_genomes galaxy_admin_api_key=YOURADMINAPIKEY". You have to create an api key yourself first in the galaxy instance. Make sure it is mapped to a user with admin rights.

Upgrading your galaxy

Using the manual: See if you can start a new fresh galaxy instance with an older bgruening/galaxy-stable version. Upgrade this to a newer version of bgruening/galaxy-stable.