Set up mongo database initialized with data from gn-mongo image:
helm install --version 4.9.1 --name gn-mongo-v0dot6 --set securityContext.enabled=false,image.repository=genomenexus/gn-mongo,image.tag=v0.6,persistence.size=20Gi stable/mongodb
Deploy genome nexus app:
kubectl apply -f gn_spring_boot.yaml
Expose as service (actual domain name binding is handled in ../ingress/README.md:
kubectl apply -f service.yaml
If you want to enable sentry, you need to provide it as a secret:
kubectl create secret generic genome-nexus-sentry-dsn --from-literal=dsn=https://sentry-key
It is referenced in the spring boot app here
Genome Nexus relies heavily on VEP. One can spin up their own version of VEP GRCh37 like this:
kubectl apply -f vep/gn_vep.yaml
It takes quite a while to start (~40m), because it downloads the VEP cache data first.
- alpine docker image doesn't play nice with kubernetes (https://twitter.com/inodb/status/999041628970127360)
- genome nexus mongo image doesn't work with chart version 4.0.0 https://github.com/helm/charts/commit/84fcbc5e6b79111baba54ff9593378cb34cae6b7