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.

Swarm functional version (wait for galaxy service to finish scanning /export before running the data loading + workflow script)

autoload.py: script implementation, easier to understand and use. small fixes to workflow.py and main.py