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Some docs improvements
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bpblanken committed Oct 16, 2024
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Expand Up @@ -37,12 +37,14 @@ mkdir -p ~/.kube; kubectl config view --raw > ~/.kube/config; chmod go-r ~/.kube
```
4. Create the [Required Secrets](#required-secrets) in your cluster using `kubectl`.
5. [Migrate](#migrating-application-data) any existing application data.
6. Install the `seqr-platform` chart with any override values:
6. Install the `seqr-platform` chart with any [override values](#valuesenvironment-overrides):
```
helm repo add seqr-helm https://broadinstitute.github.io/seqr-helm
helm install your-institution-name-seqr seqr-helm/seqr-platform -f my-values.yaml
```

You may need to run some of the above actions as super-user `sudo`, depending on your environment.

## Required Secrets

The *seqr* application expects a few secrets to be defined for the services to start. The default expected secrets are declared in the [default `values.yaml`](charts/seqr/values.yaml#L68) file of the *seqr* application chart. You should create these secrets in your kubernetes cluster prior to attempting to install the chart.
Expand All @@ -57,7 +59,7 @@ kubectl create secret generic postgres-secrets \
--from-literal=password='super-secure-password'

kubectl create secret generic seqr-secrets \
--from-literal=django_key='securely-generated-key' \
--from-literal=django_key='securely-generated-key'
```

Alternatively, you can use your preferred method for defining secrets in kubernetes. For example, you might use [External Secrets](https://external-secrets.io/) to synchronize secrets from your cloud provider into your kubernetes cluster.
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