Basic deployment docs

docs/src/content/docs/guides/getting-started.md

@@ -1,11 +1,130 @@
 ---
-title: Example Guide
-description: A guide in my new Starlight docs site.
+title: Deploying a loculus instance
+description: How to deploy a loculus instance
 ---
 
-Guides lead a user through a specific task they want to accomplish, often with a sequence of steps.
-Writing a good guide requires thinking about what your users are trying to do.
+# Prerequisites
 
-## Further reading
+Before you get started with deploying the Loculus, there are a few prerequisites you'll need to ensure are in place. 
 
-- Read [about how-to guides](https://diataxis.fr/how-to-guides/) in the Diátaxis framework
+## Kubernetes Cluster with Traefik
+
+To deploy Loculus, you'll currently need a Kubernetes cluster with Traefik installed. Kubernetes is an open-source container orchestration system that automates the deployment, scaling, and management of containerized applications. Traefik is a modern reverse proxy and load balancer that integrates seamlessly with Kubernetes.
+
+### Production Environment
+
+For a production environment, we recommend using [k3s](https://k3s.io/). K3s is a lightweight, certified Kubernetes distribution designed for production workloads.
+
+### Local Development
+
+If you're working on local development or testing, [k3d](https://k3d.io/) is a great choice. K3d allows you to run Kubernetes clusters using Docker containers. It provides a convenient way to create and manage local Kubernetes clusters for development purposes.
+
+## Helm
+
+Helm is a package manager for Kubernetes that simplifies the deployment and management of applications. It uses charts, which are packages of pre-configured Kubernetes resources, to define and install applications in a Kubernetes cluster.
+
+To deploy Loculus, you'll need to have Helm installed. Helm will be used to manage the dependencies and deploy the Loculus application using the provided Helm chart.
+
+## Sealed Secrets
+
+Sealed Secrets is a Kubernetes controller and tool for encrypting and storing sensitive information, such as passwords and API keys, as Kubernetes Secrets. It allows you to securely store and manage sensitive data in version control systems without exposing the actual values.
+
+Eventually Loculus will support various ways of managing secrets, but for now we mostly need sealed secrets. You'll need to install [Sealed Secrets](https://github.com/bitnami-labs/sealed-secrets) in your Kubernetes cluster. Sealed Secrets will be used to encrypt and manage sensitive information required by the Loculus application.
+
+## External Database (Optional)
+
+By default, the provided Helm chart will create temporary databases for testing and development purposes. These temporary databases are suitable for initial setup and experimentation.
+
+However, for a production deployment, it is highly recommended to use managed databases. (The temporary databases may be wiped at any time).
+
+To use an external database, you'll need to provide the necessary connection details, such as the database URL, username, and password. These details should be encrypted using Sealed Secrets and specified in the `values.yaml` file of the Helm chart.
+
+Here's an example of how the external database configuration might look in the `values.yaml` file:
+
+
+```yaml
+externalDatabase:
+ urlSealedSecret: "ag..."
+ usernameSealedSecret: "abc..
+ passwordSealedSecret: "abc.."
+```
+
+Make sure to replace the sealed secret values with your own encrypted values.
+
+## Clone the repository
+
+The helm chart for deploying pathoplexus is within the Loculus repo, in the `kubernetes` subdirectory. You can adjust the `kubernetes/loculus/values.yaml` file to change the default values.
+
+## Configure ingress
+
+[We need to write about how to do this]
+
+## Organism Configuration
+Loculus supports multiple organisms, each with its own configuration. The organisms section in the values.yaml file allows you to define the specific settings for each organism.
+
+Here's an example of how the organism configuration might look:
+
+
+```yaml
+organisms:
+  ebolavirus-sudan:
+    schema:
+      image: "https://cdn.britannica.com/01/179201-050-FED1B381/filamentous-ebolavirus-particles-scanning-electron-micrograph-cell.jpg?w=400&h=300&c=crop"
+      instanceName: "Ebolavirus Sudan"
+      metadata:
+        - name: date
+          type: date
+        - name: region
+          type: string
+          generateIndex: true
+          autocomplete: true
+        - name: country
+          type: string
+          generateIndex: true
+          autocomplete: true
+        - name: division
+          type: string
+          generateIndex: true
+          autocomplete: true
+        - name: host
+          type: string
+          autocomplete: true
+        - name: pango_lineage
+          type: pango_lineage
+          autocomplete: true
+          required: true
+      website:
+        tableColumns:
+          - country
+          - division
+          - date
+          - pango_lineage
+        defaultOrder: descending
+        defaultOrderBy: date
+      silo:
+        dateToSortBy: date
+        partitionBy: pango_lineage
+    preprocessing:
+      image: ghcr.io/loculus-project/preprocessing-dummy
+      args:
+        - "--watch"
+      warnings: true
+      errors: true
+      randomWarnError: true
+    referenceGenomes:
+      nucleotideSequences:
+        - name: "main"
+          sequence: "[[URL:https://cov2tree.nyc3.cdn.digitaloceanspaces.com/reference.txt]]"
+      genes: []
+```
+
+In this example, the configuration for the "ebolavirus-sudan" organism is defined. It includes schema settings, website display options, silo configuration, preprocessing details, and reference genome information.
+
+You can add multiple organisms under the organisms section, each with its own unique configuration.
+
+## Ready to Deploy?
+Once you have the prerequisites in place and have configured the `values.yaml` file according to your requirements, you're ready to deploy Loculus using the provided Helm chart.
+
+Run `helm install loculus kubernetes/loculus -f kubernetes/loculus/values.yaml`
+
+You can use `helm status loculus` to see how the deployment has gone.