Move 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.

Fix logging text. Keep species with best assembly in get_uniq_species_dict_list() (will be main jbrowse url).

Update compose files, authelia config. Fix banner. Write galaxy_nginx.conf only if needed. Modify authelia_config_path condition. Modify get config args. Remove deploy_stack_for_current_organism.instance_url

galaxy_nginx.conf jinja2 template writing, moved configuration files from 'templates' to 'files' for clarity

removed backup gspecies template file, precisions for required/optional parameters in config_example.yml

jinja2 templating for authelia and traefik entrypoint and host, gga_get_data only copies files that exist

Separated gga_load_data into a get_data part and a load part. Also handling the get_data part with specific paths and fixed some issues with the code (reworked functions and removing deprecated code).

jinja templating, more workflow changes, trying fixes for the jbrowse gmod tool using API (in progress)

run_workflow changes (functional again), some optimisation in gga_init, gga_load and run_workflow, more validation steps in gga_init