This page attempts to document the very convoluted deployment process we have for GeneNetwork. Keeping this documentation up-to-date is going to be challenging, to say the least. So, the Guix configuration for the CI/CD container should be considered the authoritative reference.
This document is for those looking for a succinct textual reference and would rather not dig through G-expressions.
TODO. Volunteers welcome!
Deployment-specific settings for genenetwork3 should be written to a configuration file and the path to that file should be set in the GN3_CONF environment variable.
Here's a typical configuration file. Please take care to customize it to your specific requirements.
SPARQL_ENDPOINT="http://localhost:9082/sparql" DATA_DIR="/export/data/genenetwork" XAPIAN_DB_PATH="/export/data/genenetwork-xapian"
DATA_DIR must contain two directories???genotype_files and synteny.