From bc8dbc8c40590c30830e179d66a6e51212165049 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 16 May 2021 17:33:15 +0200
Subject: [PATCH] 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 | 5 +++--
examples/citrus_sinensis.yml | 2 ++
examples/config.yml | 2 +-
templates/traefik_compose.yml.j2 | 2 +-
4 files changed, 7 insertions(+), 4 deletions(-)
diff --git a/README.md b/README.md
index c11b3c7..b2647cc 100755
--- a/README.md
+++ b/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
diff --git a/examples/citrus_sinensis.yml b/examples/citrus_sinensis.yml
index 0ff6d02..63483e4 100644
--- a/examples/citrus_sinensis.yml
+++ b/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
diff --git a/examples/config.yml b/examples/config.yml
index c1d5d28..cb08732 100644
--- a/examples/config.yml
+++ b/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
diff --git a/templates/traefik_compose.yml.j2 b/templates/traefik_compose.yml.j2
index c72595e..0b4634f 100644
--- a/templates/traefik_compose.yml.j2
+++ b/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:
--
GitLab