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.
1 maintainer
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