How do I run script along side a cluster instance that I am creating for configuring sql proxy using Google Deployment Manager ?
Startup scripts are not allowed to be specified for GKE nodes. From https://cloud.google.com/container-engine/reference/rest/v1/NodeConfig:
Additionally, to avoid ambiguity, keys must not conflict with any other metadata keys for the project or be one of the four reserved keys: "instance-template", "kube-env", "startup-script", and "user-data"
Take a look at https://github.com/kubernetes/contrib/tree/master/startup-script for a way to replace the functionality of startup scripts with a daemonset.