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)

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

more config options (host, passwords, tripal themes), adapted methods to handle several histories in the same instance

Modifications for multiple histories in the same gaalxy instance, some changes for swarm architecture

Deploy stacks and load data both working, only phaeoexplorer workflow script to finish. Data loading done directly from the script (not calling the container script anymore). Also some polishing.