fix authelia_db_postgres_password. Add main_species in "citrus_sinensis.yml"....

fix authelia_db_postgres_password. Add main_species in "citrus_sinensis.yml". Fix authelia_secrets_env_path in traefik_compose.yml. Update Readme

README.md

@@ -3,10 +3,11 @@
 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.
+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.
 
-Each GGA environment is deployed at [https://hostname/sp/genus_species/](https://hostname/sp/genus_species/).
+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.
 
 ## Requirements
 

examples/citrus_sinensis.yml

@@ -12,6 +12,8 @@
     strain:
     common_name:
     origin:
+    # Useful when there are multiple strains for the same species: set to "yes" to define the strain used as home for JBrowse
+    # main_species: yes
   data:
   # Paths to the different datasets to copy and import into the galaxy container (as a shared library)
   # Must be absolute paths to the dataset

examples/config.yml

@@ -8,7 +8,7 @@ proxy_ip: XXX.XXX.XXX.XXX  # Required. IP of the upstream proxy (used by Traefik
 authentication_domain_name: XXXXXXXX  #  Required for Authelia. The authentication domain name.
 authelia_config_path: /path/to/authelia_config.yml #  Required for Authelia. Path to the Authelia configuration file
 authelia_secrets_env_path: /path/to/authelia/secrets.env #  Required for Authelia. Path to the env file containing passwords and secrets needed for Authelia
-authelia-db_postgres_password: XXXXXXXX #  Required for Authelia.
+authelia_db_postgres_password: XXXXXXXX #  Required for Authelia.
 
 # galaxy-specific variables
 galaxy_default_admin_email: gga@galaxy.org  # Required

templates/traefik_compose.yml.j2

@@ -86,7 +86,7 @@ services:
       - ./authelia/:/etc/authelia/:ro
     {% if authelia_secrets_env_path is defined %}
     env_file:
-      - ./authelia/secrets.env
+      - {{authelia_secrets_env_path}}
     {% endif %}
     deploy:
       labels: