Antibody Registry

An updated version of the Antibody Registry platform

Prerequisites

Python

The deployment process is based on Python 3.9+ scripts. It is recommended to setup a virtual environment first.

With conda:

conda create --name areg python=3.9
conda activate areg

Setup CloudHarness

The Antibody Registry deployment is built on top of CloudHarness.

To setup CloudHarness:

git clone https://github.com/MetaCell/cloud-harness.git
sh cloud-harness/install.sh

Install skaffold

skaffold is needed to build the images and run them on minikube. Get it here.

Install helm

You can install helm from here.

Development setup

A Kubernetes cluster, like Minikube or Docker Desktop, is required setup locally. For more information, refer to the CloudHarness documentation

To setup the local deployment, run

harness-deployment cloud-harness . -l -d areg.local -dtls -n areg -e local -i areg-portal

With Visual Studio Code and the Cloud Code plugin installed, can run and the debug with the auto-generated configuration CloudHarness: Run/Debug.

Can also run from the command line:

skaffold dev --cleanup=false

Deploy

Create deployment

CloudHarness scripts script automate the deployment process.

To manually create the helm chart update the ci/cd Codefresh scripts, run:

harness-deployment cloud-harness . -n areg -e dev -i areg-portal
harness-deployment cloud-harness . -n areg -e prod -i areg-portal

Cluster setup

Kubernetes 1.22+ is supported (v1 spec)

Cert-manager

The cert-manager must be installed in order to use letsencrypt generated certificates

To check if cert-manager is installed, run:

kubectl get pods -n cert-manager

If cert manager is installed, the command will return 3 lines.

To install the cert manager on a new cluster, run:

kubectl apply --validate=false -f https://github.com/jetstack/cert-manager/releases/download/v0.15.1/cert-manager-legacy.yaml

See also https://cert-manager.io/docs/installation/kubernetes/.

CSI driver

On google cloud, the Compute Engine persistent disk CSI Driver must be enabled in order for the volume cloning to work.

Install and upgrade with Helm

1. Create the namespace kubectl create ns areg
2. Run helm install areg deployment/helm --namespace areg to install.
3. Run kubectl create rolebinding areg-admin-default --clusterrole=admin --serviceaccount=areg:default -n areg to allow workflows to run on namespace areg

To upgrade an existing deployment, use:

helm upgrade areg deployment/helm --namespace areg --install --reset-values [--force]

CoC

Antibody Registry adheres to the Contributor Covenant: https://www.contributor-covenant.org/

Citing Antibody Registry in academic work

Please cite as The Antibody Registry (RRID:SCR_006397) https://antibodyregistry.org/