README.md

gga_load_data tools

The gga_load_data tools allow automated deployment of GMOD visualisation tools (Chado, Tripal, JBrowse, Galaxy) for a bunch of genomes and datasets. They are based on the Galaxy Genome Annotation (GGA) project (https://galaxy-genome-annotation.github.io).

A stack of Docker services is deployed for each organism, from an input yaml file describing the data. See examples/example.yml for an example of what information can be described and the correct formatting of this input file.

Each GGA environment is deployed at https://hostname/sp/genus_species/.

Requirements

To run the gga_load_data tools, Python 3.6 and the packages listed in requirements.txt are required.

To deploy the GGA Docker services, one or multiple hosts machines are required with Docker installed, and a swarm (for cluster management and orchestration).

Reverse proxy and authentication

Traefik is a reverse proxy which allows to direct HTTP traffic to various Docker Swarm services. The Traefik dashboard is deployed at https://hostname/traefik/

Authelia is an authentication agent, which can be plugged to an LDAP server, and that Traefik can you to check permissions to access services. The authentication layer is optional. If used, the config file needs the variables https_port, authentication_domain_name, authelia_config_path.