This repository is archived. Please use the galaxyproject provided ansible roles.
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.
The galaxyproject.galaxy role should be installed and available for ansible.
| 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 |
| 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. |
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.
- hosts: servers
roles:
- role: ansible-galaxy-cluster
For a more elaborate setup check HOWTO.md.
MIT
This role has been created to maintain the LUMC Galaxy. For more information please contact the SASC team: [email protected].