Tutorial
Prerequisites
- A computer running GNU/Linux
- install Vagrant
- install VirtualBox
- Set up the prerequisites as described in the installation chapter.
Create a host to test on
- go to the galaxy-launcher repository
- go to
test/vagrant/ubuntu-16.04
- Type
vagrant up
- go to the galaxy-launcher repository
- copy the
hosts.sample
file to host
Exercise: Set up your own hosts file. Use test/hosts
as an example.
- Check if you can reach the host by
ansible -m ping HOSTNAME
(insert your own hostname here)
Create the settings files for your host.
- copy
files/example_host
tofiles/HOSTNAME
- copy
host_vars/example_host
tohost_vars/HOSTNAME
- Uncomment the commented out variables in
host_vars/HOSTNAME/galaxy_settings.yml
and change them to your preferred settings. - Use the guide on Björn Grünings page to add some settings to your galaxy that you like in
galaxy_docker_optional_environment_settings
. - Change the version of the docker image to 17.09 or whatever version you like in
host_vars/HOSTNAME/docker_settings.yml
- Install the prerequisites on your test vm by running
ansible-playbook main.yml -e "host=HOSTNAME run=install_prerequisites"
. - Install galaxy on your test VM by running
ansible-playbook main.yml -e "host=HOSTNAME run=install_galaxy"
. - Galaxy should now be accessible on localhost:8081
Provision your galaxy
Tools
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"
.
Genomes
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
Exercise:
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.