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

speciesData.py

@@ -62,7 +62,7 @@ class SpeciesData:
 
         self.date = datetime.today().strftime("%Y-%m-%d")
         self.origin = parameters_dictionary_description[constants.ORG_PARAM_DESC_ORIGIN]
-        self.performed = parameters_dictionary_data[constants.constants.ORG_PARAM_DATA_PERFORMED_BY]
+        self.performed = parameters_dictionary_data[constants.ORG_PARAM_DATA_PERFORMED_BY]
 
         if parameters_dictionary_data[constants.ORG_PARAM_DATA_GENOME_VERSION] == "":
             self.genome_version = "1.0"