Setup

In order to push/pull images from the Google container registry you must first authenticate with Google:

gcloud auth login

You then need to run a one-time setup to configure docker to use Google authentication:

gcloud auth configure-docker

Running a test

cd test
cromwell run -i oneseq_processing.inputs.BE3_small_test.json oneseq_processing.wdl 

Updating the Docker container

After modifying the Dockerfile (Docker/geomx-ngs/Dockerfile) a new image can be built locally:

cd Docker/geomx-ngs
docker build -t gcr.io/aryeelab/geomx-ngs .

If it works as expected you can commit the change to git repo. Pushing to github will trigger a new container build using Google Cloud Build. The new image is automatically stored in Google Container Registry.