Skip to content

TheJacksonLaboratory/omero-k8s-templates

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

78 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Kubernetes templates for OMERO as run at The Jackson Laboratory

The Jackson Laboratory hosts a public image repository using OMERO on Google Cloud at images.jax.org. These templates are made to mimic that OMERO deployment and related testing environments as closely as possible.

As a lightweight template repository, the current goal is to only require kubectl and either a local Kubernetes cluster or Google Cloud Project (GCP). Kustomize is used to provide multiple optional deployment configurations in the GCP yamls, run as kubectl apply -k.

Deployment overview

Schematic of OMERO deployment, explained in words below

  • One read-write OMERO server is run as an ephemeral Kubernetes pod and used for OMERO setup, data imports, and admin tasks
    • The read-write OMERO server has read-write access to the database and the NFS server with the OMERO directories. All data is imported in-place with --transfer ln_s, so image data (either on NFS or object storage) can be mounted read-only.
  • One (or more) read-only OMERO servers use a read-only database user and mount both the data and OMERO directories as read-only
  • One (or more) OMERO web deployment runs both OMERO web and Nginx and connects to the read-only OMERO server

Other relevant repositories

We are not involved with these repositories, but they are doing similar things: