diff --git a/README.md b/README.md index b2647ccccc0494e3b724f6f60264365935adc473..0e3c428a1b3a4baf19b7ebdf7e9616063bedcaf2 100755 --- a/README.md +++ b/README.md @@ -6,9 +6,25 @@ They are based on the [Galaxy Genome Annotation (GGA) project](https://galaxy-ge A stack of Docker services is deployed for each species, 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. +The services currently deployed are: +- Chado database +- Tripal: database interface and hub to all applications +- Elasticsearch: searching service used in Tripal +- JBrowse: genome browser +- Nginx proxy: page to download the data files +- Blast (optional): BLAST interface to query the data +- Galaxy: data loading orchestrator for administrators + A GGA environment is deployed for each different species at [https://hostname/sp/genus_species/](https://hostname/sp/genus_species/). Multiple strains can have the same species and are deployed in the same GGA environment. + +_**Figure** : Schematic representation of a set of Docker containers deployed with +GGA for typical genomes. Cuboids represent Docker containers. Hexagons represent different +sets of Docker containers. Blue arrows represent HTTP traffic. Gray arrows represent +data exchange performed using Galaxy tools. Black arrows represent data exchange +inherent in applications._ + ## Requirements To run the gga_load_data tools, Python 3.6 and the packages listed in [requirements.txt](./requirements.txt) are required. @@ -22,8 +38,8 @@ and a [swarm](https://docs.docker.com/engine/swarm/swarm-tutorial) (for cluster 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/](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`. +Authelia is an authentication agent, which can be plugged to an LDAP server, and that Traefik can used 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`, `authelia_secrets_env_path`, `authelia_db_postgres_password`. Authelia is accessed automatically by Traefik to check permissions everytime someones wants to access a page. If the user is not logged in, he is redirected to the authelia portal. diff --git a/images/gga_schema.png b/images/gga_schema.png new file mode 100644 index 0000000000000000000000000000000000000000..c1b55fc01176684256778e2d408450d65d1c0a7d Binary files /dev/null and b/images/gga_schema.png differ