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

utilities.py

@@ -158,7 +158,8 @@ def get_unique_species_dict_list(sp_dict_list):
 
     for sp in sp_dict_list:
         gspecies = get_gspecies_string_from_sp_dict(sp)
-        if gspecies not in unique_species_dict.keys() or sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True :
+        if gspecies not in unique_species_dict.keys() or ( constants.ORG_PARAM_DESC_MAIN_SPECIES in sp[constants.ORG_PARAM_DESC].keys() and
+                                                           sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_MAIN_SPECIES] == True ) :
             unique_species_dict[gspecies] = sp
         else:
             continue