Add support for mounting a persistent volume to the hail-search chart.
#39
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| - mountPath: {{ $.Values.environment.DATASETS_DIR }} | ||
| name: datasets | ||
| - name: mkdir-ssd-{{ $path | replace "/" "-" | replace "_" "-" | lower}} | ||
| {{- $localPath := $path | replace "SV" "SV_WGS" | replace "GCNV" "SV_WES" -}} |
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The initialization action here is copying the annotations table from the mounted volume to the in-memory volume, once per reference genome/datasetType.
| - ReadOnlyMany | ||
| resources: | ||
| requests: | ||
| storage: 2000G |
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unless we don't expect this to ever change (or if it simply needs to match the capacity attribute on the persistentvolume), i'd make this a variable as well. I don't have a strong preference here, but this unit could also be 2T (or 2Ti if you need the 1024-ish variant of a terabyte).
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🤦 this is actually a bug. I'm using {{ .Values.storageCapacity }} elsewhere in this file and just missed this one.
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the values don't need to be the same, but they might as well be for simplicity.
| labels: | ||
| {{- include "hail-search.labels" . | nindent 4 }} | ||
| spec: | ||
| storageClassName: "" |
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i'm not actually sure what happens with an empty class name specified here (i think GKE has 2 or 3 classes available by default. This could also not matter/be moot if you're just referencing persistent disks that already exist in GCE.
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this was recommended/documented somewhere in the gke docs and here... I think it's moot because the persistent disks already exist and we're not asking for dynamic provisioning
the storage classes do exist already by virtue of gke it appears:
bblanken@wmbbe-67c seqr-pipeline-airflow % kubectl get storageclass | grep pd
E0329 17:03:55.507374 11981 memcache.go:255] couldn't get resource list for external.metrics.k8s.io/v1beta1: Got empty response for: external.metrics.k8s.io/v1beta1
airflow-redis-persistence-sc pd.csi.storage.gke.io Delete Immediate true 9d
premium-rwo pd.csi.storage.gke.io Delete WaitForFirstConsumer true 9d
standard kubernetes.io/gce-pd Delete Immediate true 9d
standard-rwo (default) pd.csi.storage.gke.io Delete WaitForFirstConsumer true 9d
potentially worth re-evaluating if we're gonna support this for open-source though.
For context, we're removing our copy of hail tables from gcs to instead mount a persistent disk.