A Refget server, implemented in Python

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

Structure of the project

• The api folder contains the refget server implementation. See the README here.
• The pipeline folder contains the Nextflow pipeline for provisioning data out of Ensembl. See the README here.

How to run with Docker

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