Specialty rings

[esteinig]

Extension of the basic BRIG - like rings and annotations to some more specific applications:

• Antimicrobial resistance predictions for automatic generation of labels with abritAMR
• Probability of viral, plasmid or chromosomal origin along segments of the reference genome with geNomad
• Add styling and provide arc line specific options, add geNomad prediction class selection

For long running tasks we want to:

• Celery: adjust timeout for task result requests to 10min - if these timeout, the data is still processed and dumped into the database model, meaning while e.g. a ring is not added, on reload the updated session model is visualised
• Celery: test different settings for file uploads and long running tasks
• App: perhaps we need a job table which contains a log of submitted and completed/failed jobs maybe at a later stage, working relatively smoothly now
• Server: keep a copy of the output tagged by reference sequence or similar to avoid redundant re-computing
• Server: limit threads in case of high load on these tasks, both on Celery workers and as setting for subprocesses
• Server: limit worker container memory for tasks, or implement proper workflow scheduler for intensive pipelines
• Server Profile geNomad memory consumption to set limits on worker container

Adding the --splits argument to genomad execution to reduce memory footprint for now. See if timeout limits have to be adjusted. These arguments can all set through the FastAPI settings and when deploying the stack through the docker/brick.env stack configuration variables.

Intensive bioinformatics tasks are not meant to run in task schedulers, especially considering resource management. Need a better solution also for other projects, any suggestions welcome!