bycon 3.0.0

A Python-based environment for the GA4GH Beacon genomics API

Bycon - a Python-based full stack environment for the Beacon genomics API

The bycon project implements a data hosting environment for genomic and pheno-clinical data aligned with the GA4GH Beacon data model. It provides a Beacon API for data query and retrieval but also has extended functionality with a focus on genomic copy number variation data. For a prominent implementation example showcasing bycon features please see the Progenetix oncogenomic resource.

The underlying database system utilizes a MongoDB instance and a storage model following for the most part the GA4GH object model.

Additionally, the bycon project implements functions for the ingestion and management of genomic variants and phenoclinical data, and provides a front end for the Beacon API as a statically compiled React project ("beaconPlus"). An instance of the beaconPlus front end is accessible at beaconplus.progenetix.org.

More Documentation

Documentation has been moved to bycon.progenetix.org. Due to the rapid code development it is recommended to keep following the Changes page.

Installation

The preferred method is to modify your local configuration and then perform a package build and installation running install.sh followed by the deployment script.

The installation is also documented on the website.

bycon Libraries option 1 using ./install.sh

Since the script only copies the script directories and local configuration directory to the server path, additionally a bycon package installation is needed through either local package installation from source (install.sh in the project's root) or pip3 install bycon>=3.0.0.

bycon Libraries option 2 using pip3 install bycon

The preferred method is to modify your local configuration and then perform a package build and installation running the install.sh script followed by this deployment script.

beacon.py Server App using ./scripts/deploy.py

The install script copies the relevant bycon files to the webserver directory specified in the ../local-settings/env_paths.yaml file and sets the file permissions accordingly. By default, it requires admin permissions (sudo). If you want to run it without sudo, invoke it with --no-sudo. The current use will need to be able to write into the target directories.