Update README: add picture, list services deployed

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.
 
+![gga_schema](images/gga_schema.png)
+_**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.