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Deploy GeneNetwork

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.

genenetwork2

TODO. Volunteers welcome!

genenetwork3

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.


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