Release_2.0 next

General

• Move constants to file constants.py
• Set default config file in scripts.
• Update description of scripts in main.
• Update README.md

Input config file

• 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.

Utilities.py

• Factorize parse_input() et parse_config().
• Get input yml keys from constants (update organisms.yml.j2 and add create_org_param_dict_from_constants())

gspecies_compose.yml

• set ENABLE_WIKI and ENABLE_APOLLO to 0 in gspecies compose template
• fix ENABLE_BLAST value in gspecies compose template

gga_get_data.py

• Remove useless variable datasets_to_get

gga_init.py

• replace subprocess.call() with subprocess.run(). Factorize run_command() and run_docker_stack_deploy()
• fix banner copy

examples/config.yml

 # This is the configuration template file used by the gga_init.py, gga_load_data.py and run_workflow.py scripts
 
-# "all" section contains variables used by several services at once or the paths to import sensitive files
-all:
-      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.
+# 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:
-      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
+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:
-      tripal_password: tripalpass  # Required. Tripal database password (also used by galaxy as an environment variable)
-      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.
+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:
+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"
       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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