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

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

Cleaned up gga_init step (traefik setup and update is done separately), some changes to speciesData (use the input generator script in phaeoexplorer-tools to have the correct  attributes), trying changes to invoke workflow (WIP)

Pipeline v1.0 ready, missing orthology data and template workflows for blastp (diamond) and interpro. The data preprocessing for phaeoexplorer script is available in the phaeoexplorer-tools repo (but is not usable as a standalone)

Fixed Jbrowse workflow (removed runtime str parameter altogether) plus some formatting and code cleaning

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