Galaxy Kubernetes Boot

Use this repo to deploy Galaxy. The repo contains Ansible playbooks to prepare a cloud image and deploy a Galaxy instance. Galaxy is deployed on a Kubernetes cluster using RKE2. The playbooks work on GCP, AWS, and OpenStack (e.g., Jetstream2).

Overview

This repo is divided into two main parts:

1. Image Preparation: This part contains playbooks and scripts to prepare a cloud image with all necessary components pre-installed. See Image Preparation for details.
2. Deployment: This part contains playbooks to deploy the prepared image onto a RKE2 Kubernetes cluster. The deployment playbook can also be used without a prepared image, but using a prepared image speeds up the deployment process. Documentation for the deployment process can be found below (Note: this part of the documentation is currently out of date so will require some interpretation and adjustment).

Deployment

Prerequisites

To run the playbook we need to install Ansible and some other optional requirements that are only needed to generate the inventory file with the bin/inventory.sh script. The easiest way to install the requirements is to use pip.

python3 -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

If the host is a barebones Ubuntu, Ansible can be installed with the following commands:

sudo apt install software-properties-common
sudo add-apt-repository --yes --update ppa:ansible/ansible
sudo apt install ansible

Launching the VM

Use the provided launch script to create a VM. The script handles both persistent disk creation and existing disk attachment scenarios.

The VM uses Ubuntu 24.04 image with a root file system of at least 30GB. Security groups should have ports 22 and 80 open. The persistent disk is automatically formatted, mounted at /mnt/block_storage, and configured for the Galaxy deployment.

bin/launch_vm.sh -k "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC66Snr9..." INSTANCE_NAME

Script Parameters

• -k, --ssh-key: SSH public key for the ubuntu user (required)
• -d, --disk-name: Name of persistent disk (default: galaxy-data-INSTANCE_NAME)
• -s, --disk-size: Size of persistent disk (default: 150GB)
• -p, --project: GCP project ID (default: anvil-and-terra-development)
• -z, --zone: GCP zone (default: us-east4-c)
• -m, --machine-type: Machine type (default: e2-standard-4)
• --ephemeral-only: Create VM without persistent disk

Monitoring Deployment

After launching, you can monitor the deployment progress:

# Watch cloud-init output
gcloud compute ssh INSTANCE_NAME --command='sudo tail -f /var/log/cloud-init-output.log'

# Monitor deployment logs
gcloud compute ssh INSTANCE_NAME --command='sudo journalctl -f -u cloud-final'

Galaxy will be available at http://INSTANCE_IP/ once deployment completes (typically ~6 minutes).

Advanced: Manual VM Creation

If you prefer to use the gcloud command directly, you can do so with:

gcloud compute instances create ea-rke2-c \
  --project=anvil-and-terra-development \
  --zone=us-east4-c \
  --machine-type=e2-standard-4 \
  --image=galaxy-k8s-boot-v2025-09-26 \
  --image-project=anvil-and-terra-development \
  --boot-disk-size=100GB \
  --boot-disk-type=pd-balanced \
  --create-disk=name=galaxy-data-disk,size=150GB,type=pd-balanced,device-name=galaxy-data,auto-delete=no \
  --tags=k8s,http-server,https-server \
  --scopes=cloud-platform \
  --metadata=ssh-keys="ubuntu:ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC66Snr9/0wpnzOkseCDm5xwq8zOI3EyEh0eec0MkED32ZBCFBcS1bnuwh8ZJtjgK0lDEfMAyR9ZwBlGM+BZW1j9h62gw6OyddTNjcKpFEdC9iA6VLpaVMjiEv9HgRw3CglxefYnEefG6j7RW4J9SU1RxEHwhUUPrhNv4whQe16kKaG6P6PNKH8tj8UCoHm3WdcJRXfRQEHkjoNpSAoYCcH3/534GnZrT892oyW2cfiz/0vXOeNkxp5uGZ0iss9XClxlM+eUYA/Klv/HV8YxP7lw8xWSGbTWqL7YkWa8qoQQPiV92qmJPriIC4dj+TuDsoMjbblcgMZN1En+1NEVMbV ea_key_pair" \
  --metadata-from-file=user-data=bin/user_data.sh

For attaching an existing disk instead, use --disk=name=your-disk-name,device-name=galaxy-data,mode=rw instead of the --create-disk option.

Deleting the VM

Note: If you will want to redeploy an existing instance (ie, keep the data), before deleting it, make sure to record the ID of the Galaxy PVC. You can find it by running:

kubectl get pvc -n galaxy

Before deleting the VM, uninstall the Galaxy Helm chart to ensure all resources are properly cleaned up:

helm uninstall -n galaxy galaxy --wait
helm uninstall -n galaxy-deps galaxy-deps --wait

Then, delete the VM using:

gcloud compute instances delete INSTANCE_NAME --zone=us-east4-c [--quiet]

TODO: Update docs below. Currently out of sync with the code.

Automated deployment

There is a script that automates the deployment process available in bin/init_script.sh. The script can be supplied as user data when launching the VM and it will automatically set up the environment and run the playbook.

Generating the inventory file for manual deployment

The inventory is a file that lists the servers to be configured and defines some variables that are used in the playbooks. There is a Bash script that generates the inventory file, or it can be created manually based on the template provided. There are example inventory files in the inventories directory, but they can not be used as-is as the IP addresses and SSH keys will need to be updated.

To generate the inventory file, run the following command:

bin/inventory.sh --name my-server --ip 1.2.3.4 --key ~/.ssh/my-key.pem > inventories/my-server.ini

If running the playbook on the server itself, there is inventories/locahost file available that captures the necessary variables.

Running the playbook

Installing Galaxy

Once the inventory file is created, we can run the playbooks to deploy the Kubernetes cluster and the Galaxy instance. The playbook takes the arguments:

• chart_values_file: Optional. Path relative to values subfolder containing values that will be used to configure the Galaxy Helm chart. The default is values.yml.

ansible-playbook -i inventories/my-server.ini deploy-galaxy.yml --extra-vars "galaxy_admin_users=email@address.com"

Once the playbook completes, the Galaxy instance will be available at http://<server-ip>/ after a few minutes.

Adding users

By default, user registration is disabled on the Galaxy instance. To add users, you can use the bin/add_user.sh script. The script takes the following arguments:

• host: The IP address of the Galaxy server
• galaxy_api_key: The API key for the Galaxy admin user
• email: The email address of the Galaxy user to be added
• password: The password for the Galaxy user
• username: The username for the Galaxy user

Run the script with:

bin/add_user.sh <host> <galaxy_api_key> <email> <password> <username>

Installing Pulsar

The playbook can set up a Pulsar node instead of Galaxy. The invocation process is the same with the only difference being the application variable.

ansible-playbook -i inventories/my-server.ini playbook.yml --extra-vars "application=pulsar" --extra-vars "pulsar_api_key=changeme"

Managing the Kubernetes cluster

If you would like to manage the Kubernetes cluster, you can use the kubectl command on the server, or download the kubeconfig file from the server and use it on your local machine.

scp -i ~/.ssh/my-key.pem ubuntu@<server-ip>:/home/ubuntu/.kube/config ~/.kube/config