Monarch OLS

WARNING THIS REPO IS NO LONGER USED, NOR UPDATED

See https://github.com/monarch-initiative/ontotools-docker instead.

This repository contains the configuration of a bespoke Ontology Lookup Service for the Monarch Initiative.

To launch local in OLS via Docker

make docker-build
make docker-run

OLS should now be running at http://localhost:8080

Monarch Internal Documentation:

An overview of the process can be found here

There are 2 relevant Jenkins jobs:

• build-monarch-ols is responsible for preprocessing the ontologies, building the OLS docker image and publishing it to dockerhub.
• deploy-ols-m2 is responsible for pulling the latest monarch ols image from [dockerhub](docker pull monarchinitiative/monarch-ols) and deploying it on monarch2.

As an aside:

• hpo-pipeline-dev2 is responsible for generating the HPO daily snapshot.

Adding an ontology:

1. Add ontology metadata to ols/ols-config.yaml
2. Add ontology id to Makefile