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bpblanken committed Oct 16, 2024
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Expand Up @@ -40,10 +40,34 @@ mkdir -p ~/.kube; kubectl config view --raw > ~/.kube/config; chmod go-r ~/.kube
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
helm install YOUR_INSTITUTION_NAME-seqr seqr-helm/seqr-platform
```

You may need to run some of the above actions as super-user `sudo`, depending on your environment.
After install you should expect to something like:

```
helm install broad-seqr seqr-helm/seqr-platform
NAME: YOUR_INSTITUTION_NAME-seqr
LAST DEPLOYED: Wed Oct 16 14:50:22 2024
NAMESPACE: default
STATUS: deployed
REVISION: 1
TEST SUITE: None
```

The first deployment will include a download of all of the genomic reference data (400GB+). It is likely to be slow, but can be monitored by checking the contents of `/var/seqr/seqr-reference-data`. Once the download completes, you may check the status of the services with:

```
kubectl get pods
NAME READY STATUS RESTARTS AGE
hail-search-7678986f7-n8655 1/1 Running 0 12m34s
pipeline-runner-api-5557bbc7-vrtcj 2/2 Running 0 12m34s
pipeline-runner-ui-749c94468f-62rtv 1/1 Running 0 12m34s
seqr-68d7b855fb-bjppn 1/1 Running 0 12m34s
seqr-check-new-samples-job-28818190-vlhxj 0/1 Completed 0 12m34s
seqr-postgresql-0 1/1 Running 0 12m34s
seqr-redis-master-0 1/1 Running 0 12m34s
```

## Required Secrets

Expand Down Expand Up @@ -100,4 +124,18 @@ seqr:
GUNICORN_WORKER_THREADS: "8"
```

A more comprehensive example of what this may look like, and how the different values are formated in practice, is found in the [*seqr* unit tests](unit_test/seqr/values.yaml).
A more comprehensive example of what this may look like, and how the different values are formated in practice, is found in the [*seqr* unit tests](unit_test/seqr/values.yaml).


## Debugging FAQ
- How do I uninstall `seqr` and remove all application data?
```
helm uninstall YOUR_INSTITUTION_NAME-seqr
kind delete cluster
rm -rf /var/seqr
```
- How do I view `seqr`'s disk utilization?
You may access the size of each of the on-disk components with:
```
du -sh /var/seqr/*
```

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