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Loraine Gueguen authoredMove constants to file constants.py. Change config root to dict and update parse_config(). Change some config parameters name (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url), update example config file and compose templates. Remove apollo config variables (webapollo_user, webapollo_password) in config file and in gspecies compose template, because apollo service not deployed here. Factorize parse_input() et parse_config(). Update description of scripts in main. Set default config file in scripts. Remove useless variable datasets_to_get in gga_get_data.py. Update README.md.
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config.yml 2.18 KiB
# This is the configuration template file used by the gga_init.py, gga_load_data.py and run_workflow.py scripts
# These variables are used by several services at once or the paths to import sensitive files
hostname: localhost # Required. The hosting machine name
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: 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.
# galaxy-specific variables
galaxy_default_admin_email: gga@galaxy.org # Required
galaxy_defaut_admin_user: gga # Required
galaxy_default_admin_password: password # Required
galaxy_config_remote_user_maildomain: mydomain.com # Required. The maildomain used by Galaxy authentication
galaxy_persist_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_password: tripalpass # Required. Tripal database password (also used by galaxy as an environment variable)
tripal_banner_path: /path/to/banner.png # Optional. Use this to change the top banner in Tripal
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/" # 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"