Release 1.0

README.md

@@ -6,9 +6,28 @@ A stack of Docker services will be deployed for each organism.
 
 ## Description
 
-Automatically generates functional GGA environments from a descriptive input yaml file.
-See `examples/example.yml` for an example of what information can be described
-and the correct formatting of this input file.
+Automatically generates functional GGA environments 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/](https://hostname/sp/genus_species/).
+
+### Traefik
+
+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/)
+
+### Authentication with Authelia
+
+The authentication layer is optional. If used, the config file needs the variables `https_port`, `auth_hostname`, `authelia_config_path`.
+
+Authelia is an authentication agent, which can be plugged to an LDAP server, and that Traefik can you to check permissions to access services.
+
+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. 
+Note that Authelia needs a secured connexion (no self-signed certificate) between the upstream proxy and Traefik (and https between internet and the proxy).
+
+### Steps
 
 The "gga_load_data" tool is divided in 4 separate scripts:
 
@@ -123,8 +142,7 @@ You can check the status of the Galaxy service with `$ docker service logs -f ge
 `./serexec genus_species_galaxy supervisorctl status`.
 
 When deploying the stack of services, the Galaxy service can take a long time to be ready. This is due to the Galaxy container preparing a persistent location for the container data. 
-In development mode only, this can be bypassed by setting the variable "persist_galaxy_data" to "False" in the config file.
-
+In development mode only, this can be bypassed by setting the variable `persist_galaxy_data` to `False` in the config file.
 
 ## Requirements
 
@@ -135,3 +153,8 @@ Requires Python 3.6
 ## License
 
 [BSD 3-Clause](./LICENSE)
+
+## Acknowledgments
+
+[Anthony Bretaudeau](https://github.com/abretaud)
+[Matéo Boudet](https://github.com/mboudet)
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