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()
