Tutorial: Setup with k3d and nginx

This tutorial shows you how to set up Loculus on a plain Linux server that is reachable through a domain. For a local instance (i.e., an instance that is not publicly accessible), please check out this tutorial.

We will use k3d to run a Kubernetes cluster within Docker, nginx as a proxy server and Let’s Encrypt to obtain an SSL certificate. The tutorial was tested on an Ubuntu 24.04.

Prerequisites

• A Linux server (e.g. Ubuntu 24.04) with ideally at least 4 CPUs and 8 GB RAM
• A domain
• Install Docker: see this guide
• Install k3d: see this guide
• Install kubectl: see this guide
• Install Helm: see this guide
• Install nginx: see this guide

Step 1: Create a k3d cluster

We prepared a script that creates a k3d cluster, waits until the Traefik proxy in the cluster is ready and contains relevant port mappings. Create a file create-cluster.sh with the following content, make it executable with chmod +x create-cluster.sh and execute it with ./create-cluster.sh.

#!/bin/bash

set -euo pipefail

cluster_name="loculusCluster"

website_port_mapping="127.0.0.1:9000:30081@agent:0"
backend_port_mapping="127.0.0.1:9079:30082@agent:0"
lapis_port_mapping="127.0.0.1:9080:80@loadbalancer"
database_port_mapping="127.0.0.1:9432:30432@agent:0"
keycloak_port_mapping="127.0.0.1:9083:30083@agent:0"

if k3d cluster list | grep -q "$cluster_name"; then
    echo "Cluster $cluster_name already exists, skipping creation"
    exit 0
fi

echo "Creating cluster $cluster_name"
k3d cluster create "$cluster_name" \
    --port "$website_port_mapping" \
    --port "$backend_port_mapping" \
    --port "$lapis_port_mapping" \
    --port "$database_port_mapping" \
    --port "$keycloak_port_mapping" \
    --agents 1

is_traefik_running() {
    namespace="kube-system"
    label="app.kubernetes.io/name=traefik"
    result=$(kubectl get pods -n "$namespace" -l "$label" --no-headers 2>&1)
    if ! kubectl get pods -n "$namespace" -l "$label" --no-headers 2>&1; then
        echo "Error executing kubectl: $result"
        return 1
    fi

    if echo "$result" | grep -q "Running"; then
        return 0
    else
        return 1
    fi
}

while ! is_traefik_running; do
    echo "Waiting for Traefik to start..."
    sleep 5
done

echo "Traefik is running."

Step 2: Install secret generator

The Loculus Helm chart uses the Mittwald secrets generator. You can install it with:

helm repo add mittwald https://helm.mittwald.de
helm repo update
helm upgrade --install kubernetes-secret-generator mittwald/kubernetes-secret-generator --set secretLength=32 --set watchNamespace=""

Step 3: Configure the instance

Create a file my-values.yaml with the following configuration for the instance. Please enter your domain name (e.g., loculus.example.com), define an initial admin password and give your instance a name. This instance uses a cluster-internal test database and a very simple organism. We will improve the configuration later.

name: '<your instance name>'
host: '<your domain>'
environment: local # Do not change this: this setup uses a "local" environment as the public traffic is proxied through nginx.

runDevelopmentMainDatabase: true
runDevelopmentKeycloakDatabase: true

website:
  runtimeConfig:
    public:
      backendUrl: 'https://api.<your domain>/backend'
      lapisUrlTemplate: 'https://api.<your domain>/%organism%'
      keycloakUrl: 'https://auth.<your domain>'

auth:
  verifyEmail: false
  resetPasswordAllowed: false
  registrationAllowed: true
  smtp: null
  identityProviders: null

disableIngest: true
disableEnaSubmission: true

seqSets:
  enabled: false

secrets:
  keycloak-admin:
    type: raw
    data:
      initialAdminPassword: '<your initial admin password>'

organisms:
  angelovirus:
    schema:
      organismName: 'Angelovirus'
      metadata:
        - name: country
          type: string
          initiallyVisible: true
        - name: city
          type: string
          initiallyVisible: true
      website:
        tableColumns:
          - country
          - city
        defaultOrder: descending
        defaultOrderBy: country
    preprocessing:
      - version: 1
        image: ghcr.io/loculus-project/preprocessing-nextclade
        args:
          - 'prepro'
        configFile:
          log_level: DEBUG
          genes: []
          batch_size: 100
    referenceGenomes:
      nucleotideSequences:
        - name: 'main'
          sequence: 'NNN' # We are not performing alignment here, so this sequence doesn't matter
      genes: []

Step 4: Install and deploy

Clone the Loculus repository. The Loculus Helm chart is located in kubernetes/loculus/ and you can install it with

helm install -f my-values.yaml my-loculus loculus/kubernetes/loculus

Note

To uninstall the helm chart, you can run:

helm uninstall my-loculus

Wait a few moments until everything gets started. You can see the status of the pods with:

kubectl get pods

Once the pods are running, the website is locally available (i.e., from within the sever) at port 9000 and you can download the HTML of the landing page with:

curl localhost:9000

In the output, you should see somewhere:

<title>Home | <Your instance name></title>

Step 5: Configure DNS / domain

You have to add DNS entries of your domain to point to the server. Please add DNS entries for the following domains and sub-domains:

• <your domain>
• api.<your domain>
• auth.<your domain>

Step 6: Set up nginx

Now, you can use nginx as a reverse proxy to make the instance publicly accessible through the domain.

First, delete the default nginx page with:

sudo rm /etc/nginx/sites-enabled/default

Next, create the config for Loculus at /etc/nginx/sites-enabled/loculus with the following content and replace <your domain>:

server {
    listen 80;

    server_name <your domain>;

    location / {
        proxy_pass http://127.0.0.1:9000/;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
    }
}

server {
    listen 80;

    server_name auth.<your domain>;

    location / {
        proxy_pass http://127.0.0.1:9083/;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_buffer_size 16k;
        proxy_buffers 4 16k;
        proxy_busy_buffers_size 32k;
    }
}

server {
    listen 80;

    server_name api.<your domain>;

    location /backend/ {
        proxy_pass http://127.0.0.1:9079/;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
    }

    location / {
        proxy_pass http://127.0.0.1:9080/;
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header X-Forwarded-Proto $scheme;
    }
}

Reload nginx with

sudo service nginx reload

You should now be able to see the Loculus website at http://<your domain>. Many links and features don’t work yet as they require SSL which we describe in the next step. For example, if you click on “Login”, you should see an error.

Step 7: Set up SSL certificates

You can use certbot to obtain SSL certificates from Let’s Encrypt. To install it, run:

sudo apt install certbot python3-certbot-nginx

Now, you can request the certificates with the following command:

sudo certbot --nginx -d <your domain> -d api.<your domain> -d auth.<your domain>

You can now go back to your website at <your domain> and should be able to create an account and use the instance!

Step 8: Use a dedicated database (important for production systems)

If you want to use the instance in production, it is important to use a database outside the Loculus Helm chart. The database that the Helm chart starts is purely for test purposes and might be reset during an update.

Loculus uses PostgreSQL as its database management system and requires two databases: one for the Loculus backend, and one for the Keycloak server. Please check out the official documentation for details on how to install PostgreSQL if you don’t have one already.

Then, adapt my-values.yaml and add under the secrets key:

secrets:
  database:
    type: raw
    data:
      url: 'jdbc:postgresql://<Loculus database host>:<Loculus database port>/<Loculus database name>'
      username: '<Loculus database user>'
      password: '<Loculus database password>'
  keycloak-database:
    type: raw
    data:
      addr: '<Keycloak database host>'
      port: '<Keycloak database port>'
      database: '<Keycloak database name>'
      username: '<Keycloak database user>'
      password: '<Keycloak database password>'

To reinstall Loculus, execute:

helm uninstall my-loculus
helm install -f my-values.yaml my-loculus loculus/kubernetes/loculus

Final words

Hopefully, you now have a working Loculus instance and can start adapting it to the organisms of your needs. Please check out the Helm chart config reference for information on the available configurations.