This repository is archived. Please use the galaxyproject provided ansible roles.

ansible-galaxy-cluster

This role will set up Galaxy on a server connected to the cluster filesystem.

If you are considering reuse of this role, please checkout the Galaxy Training Nework, specifically the documentation on Galaxy server administration. This role has a very specific use case and might not solve your problem, while galaxy admin training will prepare you for a wide range of possibilities.

This role does the following:

• Makes sure all necessary components of galaxy are available on the cluster filesystem.
• Installs python on the cluster filesystem (using conda) and utilizes this to create the galaxy virtual environment. This ensures all nodes on the cluster utilize the same python binary for tasks that require the galaxy virtualenv.
• uses the galaxyproject.galaxy role to install galaxy. Sets all the defaults necessary.
• Installs docker and sets up postgres and nginx on the server using docker.
• Sets up galaxy as a systemd service
• Sets up a systemd timer service that regularly makes a SQL dump of the database.

Not included:

• configuring job_conf.xml, checkout the galaxyproject.galaxy role for documentation on how to add configuration files. Checkout the advanced job_conf example for information on how to setup galaxy for your cluster.

For an example check HOWTO.md.

Requirements

The galaxyproject.galaxy role should be installed and available for ansible.

Role Variables

Important variables

Variable	default	description
galaxy_cluster_dir	/cluster/galaxy	Location on the cluster where galaxy should be installed.
galaxy_python_version	"3.7"	Which python version should be used to install galaxy
galaxy_server_key	REQUIRED	The SSL server key.
galaxy_server_cert	REQUIRED	The SSL server certificate

Other variables

Variable	default	description
galaxy_db_username	galaxy	Username for the galaxy database
galaxy_db_name	galaxy	The name of the galaxy database
galaxy_minicoda_download_url	https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh	The default download url for miniconda.
galaxy_miniconda_download_location	/tmp/miniconda.sh	Where to store the conda install script.
`nginx_dhparam_bits	4096	Nginx is more secure when a dhparam file is generated. Set the amount of bits for the generation.
nginx_ssl_dir	/etc/nginx/ssl	where the dhparam files are stored
docker_service_nginx_image	nginx:stable	Image used for nginx
`docker_service_postgres_image	postgres:latest	Image used for postgres
galaxy_backup_dir	/var/lib/galaxy/database_backup	Where to store the SQL dump of the database.
galaxy_backup_calendar	daily	Set backup timer schedule, see https://www.freedesktop.org/software/systemd/man/systemd.time.html#Calendar%20Events
galaxy_backup_max_copies	1	How many SQL dumps should be kept on the server.

Dependencies

The galaxyproject.galaxy role is what is used to install galaxy. Checkout the documentation of this role for more information on how to apply the necessary settings to your galaxy.

Example Playbook

- hosts: servers
  roles:
     - role: ansible-galaxy-cluster

For a more elaborate setup check HOWTO.md.

License

MIT

Author Information

This role has been created to maintain the LUMC Galaxy. For more information please contact the SASC team: [email protected].