release 1.0.1

• copy nginx conf from file or template
• define required param in config_example.yml
• fix species folder name (remove -)
• fix mount of unused galaxy_data_libs.py in docker-compose file

examples/config_example.yml

@@ -2,28 +2,28 @@
 
 # "all" section contains variables used by several services at once or the paths to import sensitive files
 all:
-      hostname: localhost  # The hosting machine name
-      dashboard_port: 8001  # The desired port (on the hosting machine) for the traefik container dashboard
-      http_port: 8888  # The HTTP port docker will use on the hosting machine 
-      https_port: 8889  # The HTTPS port docker will use on the hosting machine. Required for Authelia
-      proxy_ip: XXXXXXXXXXXX  # IP of the upstream proxy (used by Traefik)
-      auth_hostname: XXXXXXXXXXXX  #  Required for Authelia. The authentication domain name.
+      hostname: localhost  # Required. The hosting machine name
+      dashboard_port: 8001  # Required. The desired port (on the hosting machine) for the traefik container dashboard
+      http_port: 8888  # Required. The HTTP port docker will use on the hosting machine 
+      https_port: 8889  # Required for Authelia. The HTTPS port docker will use on the hosting machine
+      proxy_ip: XXXXXXXXXXXX  # Required. IP of the upstream proxy (used by Traefik)
+      authentication_domain_name: XXXXXXXXXXXX  #  Required for Authelia. The authentication domain name.
       authelia_config_path: /path/to/authelia_config.yml #  Required for Authelia. Path to the Authelia configuration file
 # galaxy-specific variables
 galaxy:
-      galaxy_default_admin_email: gga@galaxy.org
-      galaxy_defaut_admin_user: gga
-      galaxy_default_admin_password: password
-      webapollo_user: admin_apollo@galaxy.org
-      webapollo_password: apollopass
-      galaxy_config_remote_user_maildomain: mydomain.com  # The maildomain used by Galaxy authentication
-      persist_galaxy_data: "True"  # Optional. If True, docker data will be backed up. Do not set this variable to "false" for production
+      galaxy_default_admin_email: gga@galaxy.org  # Required
+      galaxy_defaut_admin_user: gga  # Required
+      galaxy_default_admin_password: password  # Required
+      webapollo_user: admin_apollo@galaxy.org  # Required
+      webapollo_password: apollopass  # Required
+      galaxy_config_remote_user_maildomain: mydomain.com  # Required. The maildomain used by Galaxy authentication
+      persist_galaxy_data: "True"  # # Optional (default: True). If False, docker data will NOT be persisted on your host's file system and will be lost any time the galaxy container is recreated. Do not set this variable to "False" for production
 # tripal-specific variables
 tripal:
-      tripal_password: tripalpass  # Tripal database password (also used by galaxy as an environment variable)
+      tripal_password: tripalpass  # Required. Tripal database password (also used by galaxy as an environment variable)
       banner_path: /my/path/banner.png  # Optional. Custom banner path 
       tripal_theme_name: tripal_gga   # Optional. Use this to use another theme
       tripal_theme_git_clone: http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_gga.git  # Optional. Use this to install another theme.
 # jbrowse-specific variables
 jbrowse:
-      menu_url: "http://localhost:8888/" # Used with run_workflow_phaeoexplorer.py. If present, this variable is used to define jbrowse menu_url, if absent, will use https://hostname:https_port instead
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+      menu_url: "http://localhost:8888/" # Optional. Used with run_workflow_phaeoexplorer.py: if present, this variable is used to define JBrowse menu_url (to define the template url for the JBrowse feature's link to Tripal), if absent, will use default "https://hostname"
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