candig/htsget_app

Htsget API implementation based on the Htsget protocol

Htsget Application

Htsget API implementation that is based on the Htsget retrieval API specifications.

Access to the underlying data objects is mediated through a "baby DRS" server which runs as a separate REST API. The OpenAPI file specifies a suggested format for DRS-compliant genomic variant, read, and index objects. Hopefully a compatible, separate DRS server will be able to implement this API as-is.

Thank you to gel-htsget for being a good starting point to this project

Stack

• Connexion for implementing the API
• PostgreSQL
• ga4gh Data-Repository-Service(DRS)
• minio-py
• Flask
• Python 3
• Pysam
• Pytest
• Travis-CI

Installation

The server software can be installed in a virtual environment:

python setup.py install

Running

This application can be configured by way of the config.ini file in the root of the project. The server can be run with:

python htsget_server/server.py

This application can also be set up in a docker container. A docker-compose file and Dockerfile are provided.

The default MinIO location specified in the config.ini file is the sandbox at MinIO, but a different location can be specified there as well. Be sure to update the access key and secret key values in config.ini.

Testing

For testing, a small test suite under tests/test_htsget_server.py can be run by starting the server and running:

pytest

For automated testing, activate the repo with Travis-CI