A Refget server, implemented in Python

This is a REST API server, conforming to the Refget specification It is implemented with Python and Fastapi.

Please also see the README file for the refget app here.

How to run with Docker

Two docker files are provided, one for nginx-unit and one for Uvicorn. Choose one, build the Docker image, then run it:

docker build --tag=refget-app .
docker run -it --mount type=bind,src=/anypath/,dst=/www/unit/data -p 8000:8000 refget-app:latest

If data is mounted to a different path in the container, the env variables INDEXDBPATH and SEQPATH must be set accordingly.

Data

This app expects data with this layout:

anypath/
anypath/indexdb.tkh
anypath/<genome_uuid>/
anypath/<genome_uuid>/seqs/
anypath/<genome_uuid>/seqs/seq.txt.zst
anypath/<genome_uuid>/seqs/cdna.txt.zst
anypath/<genome_uuid>/seqs/cds.txt.zst
anypath/<genome_uuid>/seqs/pep.txt.zst