From 502ab7df2dbc7c3253202c3a57d55706a9df4a9f Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Thu, 16 Apr 2026 15:27:23 -0700
Subject: [PATCH 1/9] feat: remove redis

---
 README.md                                     |  2 +-
 Tiltfile                                      |  6 +-
 manifests/db/redis.yaml                       | 72 -------------------
 manifests/migration.yaml                      |  2 -
 manifests/virtool/base/deployment.yaml        |  2 -
 manifests/workflows/build-index.yaml          |  5 --
 manifests/workflows/create-sample.yaml        |  5 --
 manifests/workflows/create-subtraction.yaml   |  5 --
 manifests/workflows/iimi.yaml                 |  5 --
 manifests/workflows/kustomization.yaml        |  3 -
 manifests/workflows/nuvs.yaml                 |  5 --
 manifests/workflows/patches/patch-json.yaml   | 18 -----
 .../workflows/patches/patch-trigger.yaml      | 15 ----
 manifests/workflows/pathoscope.yaml           |  5 --
 14 files changed, 3 insertions(+), 147 deletions(-)
 delete mode 100644 manifests/db/redis.yaml
 delete mode 100644 manifests/workflows/patches/patch-trigger.yaml

diff --git a/README.md b/README.md
index 05a6385..e048f1e 100644
--- a/README.md
+++ b/README.md
@@ -62,7 +62,7 @@
    ```
 
    Tilt manages the Kubernetes development environment. It starts all necessary services
-   (KEDA, MongoDB, PostgreSQL, Redis) and the Virtool workloads and services.
+   (KEDA, MongoDB, PostgreSQL) and the Virtool workloads and services.
 
 ## Tilt
 
diff --git a/Tiltfile b/Tiltfile
index 9eb04ce..11c99d9 100644
--- a/Tiltfile
+++ b/Tiltfile
@@ -27,7 +27,6 @@ helm_resource(
 
 k8s_yaml('manifests/db/mongo.yaml')
 k8s_yaml('manifests/db/postgres.yaml')
-k8s_yaml('manifests/db/redis.yaml')
 k8s_yaml('manifests/storage.yaml')
 
 k8s_resource(
@@ -40,7 +39,6 @@ k8s_resource(
 
 k8s_resource("mongo", labels=['data'])
 k8s_resource("postgres", labels=['data'])
-k8s_resource('redis', labels=['data'])
 
 if 'migration' in to_edit:
     docker_build('ghcr.io/virtool/migration', '../virtool-migration/')
@@ -102,7 +100,7 @@ k8s_resource(
     'virtool-migration',
     labels=['virtool'],
     new_name="migration",
-    resource_deps=["mongo", "postgres", "redis", "storage"],
+    resource_deps=["mongo", "postgres", "storage"],
     trigger_mode=TRIGGER_MODE_MANUAL
 )
 
@@ -173,7 +171,7 @@ k8s_kind(
 
 k8s_yaml(kustomize('manifests/workflows'))
 
-scaled_job_deps = ['keda', 'redis']
+scaled_job_deps = ['keda']
 
 k8s_resource(
     "virtool-workflow-build-index",
diff --git a/manifests/db/redis.yaml b/manifests/db/redis.yaml
deleted file mode 100644
index 3972f30..0000000
--- a/manifests/db/redis.yaml
+++ /dev/null
@@ -1,72 +0,0 @@
-apiVersion: apps/v1
-kind: StatefulSet
-metadata:
-  name: redis
-  labels:
-    app: redis
-spec:
-  serviceName: redis
-  replicas: 1
-  selector:
-    matchLabels:
-      app: redis
-  template:
-    metadata:
-      labels:
-        app: redis
-    spec:
-      containers:
-        - image: redis:8
-          name: redis
-          imagePullPolicy: Always
-          args:
-            - --requirepass
-            - virtool
-          resources:
-            requests:
-              cpu: 250m
-              memory: 256Mi
-            limits:
-              cpu: 375m
-              memory: 384Mi
-          readinessProbe:
-            exec:
-              command:
-                - redis-cli
-                - -a
-                - virtool
-                - ping
-            initialDelaySeconds: 5
-            periodSeconds: 10
-          livenessProbe:
-            exec:
-              command:
-                - redis-cli
-                - -a
-                - virtool
-                - ping
-            initialDelaySeconds: 10
-            periodSeconds: 10
-          volumeMounts:
-            - name: data
-              mountPath: /data
-  volumeClaimTemplates:
-    - metadata:
-        name: data
-      spec:
-        accessModes: ["ReadWriteOnce"]
-        resources:
-          requests:
-            storage: 5Gi
----
-apiVersion: v1
-kind: Service
-metadata:
-  name: redis
-spec:
-  selector:
-    app: redis
-  ports:
-    - protocol: TCP
-      port: 6379
-      targetPort: 6379
diff --git a/manifests/migration.yaml b/manifests/migration.yaml
index 74c978e..1c5b328 100644
--- a/manifests/migration.yaml
+++ b/manifests/migration.yaml
@@ -27,8 +27,6 @@ spec:
               value: "mongodb://virtool:virtool@mongo.default.svc.cluster.local/virtool"
             - name: VT_POSTGRES_CONNECTION_STRING
               value: "postgresql+asyncpg://virtool@postgres.default.svc.cluster.local?password=virtool"
-            - name: VT_REDIS_CONNECTION_STRING
-              value: "redis://:virtool@redis.default.svc.cluster.local"
           imagePullPolicy: Always
           resources:
             limits:
diff --git a/manifests/virtool/base/deployment.yaml b/manifests/virtool/base/deployment.yaml
index da836f8..7918a7f 100644
--- a/manifests/virtool/base/deployment.yaml
+++ b/manifests/virtool/base/deployment.yaml
@@ -21,8 +21,6 @@ spec:
               value: "0.0.0.0"
             - name: VT_MONGODB_CONNECTION_STRING
               value: "mongodb://virtool:virtool@mongo.default.svc.cluster.local/virtool"
-            - name: VT_REDIS_CONNECTION_STRING
-              value: "redis://:virtool@redis.default.svc.cluster.local"
             - name: VT_POSTGRES_CONNECTION_STRING
               value: "postgresql+asyncpg://virtool@postgres.default.svc.cluster.local?password=virtool"
           ports:
diff --git a/manifests/workflows/build-index.yaml b/manifests/workflows/build-index.yaml
index d2f2a7f..571ed14 100644
--- a/manifests/workflows/build-index.yaml
+++ b/manifests/workflows/build-index.yaml
@@ -20,8 +20,6 @@ spec:
                 value: "2"
               - name: VT_MEM
                 value: "2"
-              - name: VT_REDIS_LIST_NAME
-                value: "jobs_build_index"
             resources:
               limits:
                 cpu: 3
@@ -29,6 +27,3 @@ spec:
               requests:
                 cpu: 3
                 memory: 5Gi
-  triggers:
-  - metadata:
-      listName: "jobs_build_index"
diff --git a/manifests/workflows/create-sample.yaml b/manifests/workflows/create-sample.yaml
index c28516b..bf24ac2 100644
--- a/manifests/workflows/create-sample.yaml
+++ b/manifests/workflows/create-sample.yaml
@@ -20,8 +20,6 @@ spec:
                 value: "2"
               - name: VT_MEM
                 value: "4"
-              - name: VT_REDIS_LIST_NAME
-                value: "jobs_create_sample"
             resources:
               limits:
                 cpu: 2700m
@@ -29,6 +27,3 @@ spec:
               requests:
                 cpu: 2700m
                 memory: 5Gi
-  triggers:
-  - metadata:
-      listName: "jobs_create_sample"
diff --git a/manifests/workflows/create-subtraction.yaml b/manifests/workflows/create-subtraction.yaml
index b4ba2f3..0e902fd 100644
--- a/manifests/workflows/create-subtraction.yaml
+++ b/manifests/workflows/create-subtraction.yaml
@@ -20,8 +20,6 @@ spec:
                 value: "2"
               - name: VT_MEM
                 value: "2"
-              - name: VT_REDIS_LIST_NAME
-                value: "jobs_create_subtraction"
             resources:
               limits:
                 cpu: "3"
@@ -29,6 +27,3 @@ spec:
               requests:
                 cpu: "3"
                 memory: 5Gi
-  triggers:
-  - metadata:
-      listName: "jobs_create_subtraction"
diff --git a/manifests/workflows/iimi.yaml b/manifests/workflows/iimi.yaml
index 54e2d48..47649d1 100644
--- a/manifests/workflows/iimi.yaml
+++ b/manifests/workflows/iimi.yaml
@@ -20,8 +20,6 @@ spec:
                 value: "4"
               - name: VT_PROC
                 value: "10"
-              - name: VT_REDIS_LIST_NAME
-                value: "jobs_iimi"
             resources:
               limits:
                 cpu: "5"
@@ -29,6 +27,3 @@ spec:
               requests:
                 cpu: "5"
                 memory: 11Gi
-  triggers:
-  - metadata:
-      listName: "jobs_iimi"
diff --git a/manifests/workflows/kustomization.yaml b/manifests/workflows/kustomization.yaml
index d948a9e..cf828cc 100644
--- a/manifests/workflows/kustomization.yaml
+++ b/manifests/workflows/kustomization.yaml
@@ -14,9 +14,6 @@ patches:
   - path: patches/patch-json.yaml
     target:
       kind: ScaledJob
-  - path: patches/patch-trigger.yaml
-    target:
-      kind: ScaledJob
 
 resources:
   - build-index.yaml
diff --git a/manifests/workflows/nuvs.yaml b/manifests/workflows/nuvs.yaml
index 912df5b..8643ee7 100644
--- a/manifests/workflows/nuvs.yaml
+++ b/manifests/workflows/nuvs.yaml
@@ -17,8 +17,6 @@ spec:
                 value: "4"
               - name: VT_MEM
                 value: "10"
-              - name: VT_REDIS_LIST_NAME
-                value: "jobs_nuvs"
             resources:
               limits:
                 cpu: "5"
@@ -26,6 +24,3 @@ spec:
               requests:
                 cpu: "4"
                 memory: 10Gi
-  triggers:
-  - metadata:
-      listName: "jobs_nuvs"
\ No newline at end of file
diff --git a/manifests/workflows/patches/patch-json.yaml b/manifests/workflows/patches/patch-json.yaml
index 8427a5e..107de52 100644
--- a/manifests/workflows/patches/patch-json.yaml
+++ b/manifests/workflows/patches/patch-json.yaml
@@ -8,24 +8,6 @@
     name: VT_JOBS_API_CONNECTION_STRING
     value: http://virtool-api-jobs-service.default.svc.cluster.local
 
-- op: add
-  path: /spec/jobTargetRef/template/spec/containers/0/env/-1
-  value:
-    name: VT_REDIS_CONNECTION_STRING
-    value: redis://:virtool@redis.default.svc.cluster.local
-
-- op: add
-  path: /spec/jobTargetRef/template/spec/containers/0/env/-1
-  value:
-    name: VT_REDIS_HOST
-    value: redis.default.svc.cluster.local:6379
-
-- op: add
-  path: /spec/jobTargetRef/template/spec/containers/0/env/-1
-  value:
-    name: VT_REDIS_PASSWORD
-    value: virtool
-
 - op: add
   path: /spec/jobTargetRef/template/spec/containers/0/env/-1
   value:
diff --git a/manifests/workflows/patches/patch-trigger.yaml b/manifests/workflows/patches/patch-trigger.yaml
deleted file mode 100644
index fee4b13..0000000
--- a/manifests/workflows/patches/patch-trigger.yaml
+++ /dev/null
@@ -1,15 +0,0 @@
-- op: add
-  path: /spec/triggers/0/type
-  value: redis
-
-- op: add
-  path: /spec/triggers/0/metadata/address
-  value: redis.default.svc.cluster.local:6379
-
-- op: add
-  path: /spec/triggers/0/metadata/passwordFromEnv
-  value: VT_REDIS_PASSWORD
-
-- op: add
-  path: /spec/triggers/0/metadata/listLength
-  value: "1"
diff --git a/manifests/workflows/pathoscope.yaml b/manifests/workflows/pathoscope.yaml
index 7ad7bcf..d0fd4f1 100644
--- a/manifests/workflows/pathoscope.yaml
+++ b/manifests/workflows/pathoscope.yaml
@@ -17,8 +17,6 @@ spec:
                 value: "8"
               - name: VT_PROC
                 value: "4"
-              - name: VT_REDIS_LIST_NAME
-                value: "jobs_pathoscope_bowtie"
             resources:
               limits:
                 cpu: "5"
@@ -26,6 +24,3 @@ spec:
               requests:
                 cpu: "5"
                 memory: 10Gi
-  triggers:
-  - metadata:
-      listName: "jobs_pathoscope_bowtie"

From 5a0422b6a97bde488678e621367c0d6c3ed128bc Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Thu, 16 Apr 2026 15:51:46 -0700
Subject: [PATCH 2/9] feat: scale workflows via jobs counts api

Replace the removed redis-list KEDA triggers with per-workflow
metrics-api triggers that poll /jobs/v2/counts on the web api and
scale on the pending count for each workflow.

Add api-web to scaled_job_deps in Tiltfile so ScaledJobs come up
after the endpoint is reachable.
---
 Tiltfile                                    | 2 +-
 manifests/workflows/build-index.yaml        | 7 +++++++
 manifests/workflows/create-sample.yaml      | 7 +++++++
 manifests/workflows/create-subtraction.yaml | 7 +++++++
 manifests/workflows/iimi.yaml               | 7 +++++++
 manifests/workflows/nuvs.yaml               | 7 +++++++
 manifests/workflows/pathoscope.yaml         | 7 +++++++
 7 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/Tiltfile b/Tiltfile
index 11c99d9..bad7a2f 100644
--- a/Tiltfile
+++ b/Tiltfile
@@ -171,7 +171,7 @@ k8s_kind(
 
 k8s_yaml(kustomize('manifests/workflows'))
 
-scaled_job_deps = ['keda']
+scaled_job_deps = ['keda', 'api-web']
 
 k8s_resource(
     "virtool-workflow-build-index",
diff --git a/manifests/workflows/build-index.yaml b/manifests/workflows/build-index.yaml
index 571ed14..dc8c9ef 100644
--- a/manifests/workflows/build-index.yaml
+++ b/manifests/workflows/build-index.yaml
@@ -27,3 +27,10 @@ spec:
               requests:
                 cpu: 3
                 memory: 5Gi
+  triggers:
+    - type: metrics-api
+      metadata:
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        valueLocation: "pending.build_index"
+        targetValue: "1"
+        activationTargetValue: "0"
diff --git a/manifests/workflows/create-sample.yaml b/manifests/workflows/create-sample.yaml
index bf24ac2..95024c3 100644
--- a/manifests/workflows/create-sample.yaml
+++ b/manifests/workflows/create-sample.yaml
@@ -27,3 +27,10 @@ spec:
               requests:
                 cpu: 2700m
                 memory: 5Gi
+  triggers:
+    - type: metrics-api
+      metadata:
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        valueLocation: "pending.create_sample"
+        targetValue: "1"
+        activationTargetValue: "0"
diff --git a/manifests/workflows/create-subtraction.yaml b/manifests/workflows/create-subtraction.yaml
index 0e902fd..399dafe 100644
--- a/manifests/workflows/create-subtraction.yaml
+++ b/manifests/workflows/create-subtraction.yaml
@@ -27,3 +27,10 @@ spec:
               requests:
                 cpu: "3"
                 memory: 5Gi
+  triggers:
+    - type: metrics-api
+      metadata:
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        valueLocation: "pending.create_subtraction"
+        targetValue: "1"
+        activationTargetValue: "0"
diff --git a/manifests/workflows/iimi.yaml b/manifests/workflows/iimi.yaml
index 47649d1..f00de29 100644
--- a/manifests/workflows/iimi.yaml
+++ b/manifests/workflows/iimi.yaml
@@ -27,3 +27,10 @@ spec:
               requests:
                 cpu: "5"
                 memory: 11Gi
+  triggers:
+    - type: metrics-api
+      metadata:
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        valueLocation: "pending.iimi"
+        targetValue: "1"
+        activationTargetValue: "0"
diff --git a/manifests/workflows/nuvs.yaml b/manifests/workflows/nuvs.yaml
index 8643ee7..a96085b 100644
--- a/manifests/workflows/nuvs.yaml
+++ b/manifests/workflows/nuvs.yaml
@@ -24,3 +24,10 @@ spec:
               requests:
                 cpu: "4"
                 memory: 10Gi
+  triggers:
+    - type: metrics-api
+      metadata:
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        valueLocation: "pending.nuvs"
+        targetValue: "1"
+        activationTargetValue: "0"
diff --git a/manifests/workflows/pathoscope.yaml b/manifests/workflows/pathoscope.yaml
index d0fd4f1..57747c2 100644
--- a/manifests/workflows/pathoscope.yaml
+++ b/manifests/workflows/pathoscope.yaml
@@ -24,3 +24,10 @@ spec:
               requests:
                 cpu: "5"
                 memory: 10Gi
+  triggers:
+    - type: metrics-api
+      metadata:
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        valueLocation: "pending.pathoscope"
+        targetValue: "1"
+        activationTargetValue: "0"

From 74ec520c52cb980faa2e4ca643f1b5f3852e0aa6 Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Mon, 20 Apr 2026 19:49:01 -0700
Subject: [PATCH 3/9] feat: use garage

Run the bucket/key bootstrap as a native sidecar inside the garage
pod instead of a separate Job. Sidecar readiness gates pod readiness
so dependents only proceed after bootstrap completes.
---
 Tiltfile                                    |   4 +-
 manifests/db/garage.yaml                    | 169 ++++++++++++++++++++
 manifests/migration.yaml                    |   2 +-
 manifests/ui/kustomization.yaml             |   2 +-
 manifests/virtool/base/kustomization.yaml   |   2 +-
 manifests/workflows/build-index.yaml        |   6 +-
 manifests/workflows/create-sample.yaml      |   6 +-
 manifests/workflows/create-subtraction.yaml |   6 +-
 manifests/workflows/iimi.yaml               |   4 +-
 manifests/workflows/nuvs.yaml               |   6 +-
 manifests/workflows/pathoscope.yaml         |   6 +-
 11 files changed, 198 insertions(+), 15 deletions(-)
 create mode 100644 manifests/db/garage.yaml

diff --git a/Tiltfile b/Tiltfile
index bad7a2f..07819a9 100644
--- a/Tiltfile
+++ b/Tiltfile
@@ -25,6 +25,7 @@ helm_resource(
     resource_deps=['kedacore']
 )
 
+k8s_yaml('manifests/db/garage.yaml')
 k8s_yaml('manifests/db/mongo.yaml')
 k8s_yaml('manifests/db/postgres.yaml')
 k8s_yaml('manifests/storage.yaml')
@@ -37,6 +38,7 @@ k8s_resource(
     labels=['data']
 )
 
+k8s_resource("garage", labels=['data'])
 k8s_resource("mongo", labels=['data'])
 k8s_resource("postgres", labels=['data'])
 
@@ -100,7 +102,7 @@ k8s_resource(
     'virtool-migration',
     labels=['virtool'],
     new_name="migration",
-    resource_deps=["mongo", "postgres", "storage"],
+    resource_deps=["garage", "mongo", "postgres", "storage"],
     trigger_mode=TRIGGER_MODE_MANUAL
 )
 
diff --git a/manifests/db/garage.yaml b/manifests/db/garage.yaml
new file mode 100644
index 0000000..d829350
--- /dev/null
+++ b/manifests/db/garage.yaml
@@ -0,0 +1,169 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: garage-config
+data:
+  garage.toml: |
+    metadata_dir = "/var/lib/garage/meta"
+    data_dir = "/var/lib/garage/data"
+    db_engine = "sqlite"
+    replication_factor = 1
+    rpc_bind_addr = "[::]:3901"
+    rpc_public_addr = "garage:3901"
+    rpc_secret = "1111111111111111111111111111111111111111111111111111111111111111"
+
+    [s3_api]
+    s3_region = "garage"
+    api_bind_addr = "[::]:3900"
+    root_domain = ".s3.garage"
+
+    [admin]
+    api_bind_addr = "[::]:3903"
+    admin_token = "virtool-dev-admin-token"
+---
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: garage-init-script
+data:
+  init.sh: |
+    #!/bin/sh
+    set -eu
+
+    ADMIN_URL="http://garage:3903"
+    AUTH="Authorization: Bearer virtool-dev-admin-token"
+    BUCKET="virtool"
+    ACCESS_KEY_ID="GK000000000000000000000001"
+    SECRET_ACCESS_KEY="0000000000000000000000000000000000000000000000000000000000000001"
+
+    apk add --no-cache curl jq >/dev/null
+
+    until curl -sf -H "${AUTH}" "${ADMIN_URL}/health" >/dev/null; do sleep 1; done
+
+    NODE_ID=$(curl -sf -H "${AUTH}" "${ADMIN_URL}/v1/status" | jq -r '.node')
+    CURRENT_VERSION=$(curl -sf -H "${AUTH}" "${ADMIN_URL}/v1/layout" | jq -r '.version')
+
+    if [ "${CURRENT_VERSION}" = "0" ]; then
+      curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
+        -d "[{\"id\":\"${NODE_ID}\",\"zone\":\"dc1\",\"capacity\":1000000000,\"tags\":[]}]" \
+        "${ADMIN_URL}/v1/layout" >/dev/null
+      curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
+        -d '{"version":1}' "${ADMIN_URL}/v1/layout/apply" >/dev/null
+    fi
+
+    BUCKET_ID=$(curl -s -H "${AUTH}" "${ADMIN_URL}/v1/bucket?globalAlias=${BUCKET}" | jq -r '.id // empty')
+    if [ -z "${BUCKET_ID}" ]; then
+      BUCKET_ID=$(curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
+        -d "{\"globalAlias\":\"${BUCKET}\"}" "${ADMIN_URL}/v1/bucket" | jq -r '.id')
+    fi
+
+    EXISTING_KEY=$(curl -s -H "${AUTH}" "${ADMIN_URL}/v1/key?id=${ACCESS_KEY_ID}" | jq -r '.accessKeyId // empty')
+    if [ -z "${EXISTING_KEY}" ]; then
+      curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
+        -d "{\"accessKeyId\":\"${ACCESS_KEY_ID}\",\"secretAccessKey\":\"${SECRET_ACCESS_KEY}\",\"name\":\"virtool-dev-key\"}" \
+        "${ADMIN_URL}/v1/key/import" >/dev/null
+    fi
+
+    curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
+      -d "{\"bucketId\":\"${BUCKET_ID}\",\"accessKeyId\":\"${ACCESS_KEY_ID}\",\"permissions\":{\"read\":true,\"write\":true,\"owner\":false}}" \
+      "${ADMIN_URL}/v1/bucket/allow" >/dev/null
+
+    echo "garage bootstrap ok: bucket=${BUCKET} key=${ACCESS_KEY_ID}"
+---
+apiVersion: apps/v1
+kind: StatefulSet
+metadata:
+  name: garage
+spec:
+  serviceName: "garage"
+  replicas: 1
+  selector:
+    matchLabels:
+      app: garage
+  template:
+    metadata:
+      labels:
+        app: garage
+    spec:
+      initContainers:
+        - name: garage-init
+          image: alpine:3.20
+          restartPolicy: Always
+          command: ["/bin/sh", "-c", "/scripts/init.sh && touch /tmp/ready && exec sleep infinity"]
+          resources:
+            requests:
+              cpu: 50m
+              memory: 32Mi
+            limits:
+              cpu: 100m
+              memory: 64Mi
+          readinessProbe:
+            exec:
+              command: ["test", "-f", "/tmp/ready"]
+            periodSeconds: 2
+          volumeMounts:
+            - name: init-script
+              mountPath: /scripts
+      containers:
+        - name: garage
+          image: dxflrs/garage:v1.1.0
+          ports:
+            - containerPort: 3900
+            - containerPort: 3903
+          resources:
+            requests:
+              cpu: 100m
+              memory: 128Mi
+            limits:
+              cpu: 250m
+              memory: 256Mi
+          readinessProbe:
+            httpGet:
+              path: /health
+              port: 3903
+            initialDelaySeconds: 2
+            periodSeconds: 5
+          volumeMounts:
+            - name: config
+              mountPath: /etc/garage.toml
+              subPath: garage.toml
+            - name: meta
+              mountPath: /var/lib/garage/meta
+            - name: data
+              mountPath: /var/lib/garage/data
+      volumes:
+        - name: config
+          configMap:
+            name: garage-config
+        - name: init-script
+          configMap:
+            name: garage-init-script
+            defaultMode: 0755
+  volumeClaimTemplates:
+    - metadata:
+        name: meta
+      spec:
+        accessModes: ["ReadWriteOnce"]
+        resources:
+          requests:
+            storage: 1Gi
+    - metadata:
+        name: data
+      spec:
+        accessModes: ["ReadWriteOnce"]
+        resources:
+          requests:
+            storage: 5Gi
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: garage
+spec:
+  selector:
+    app: garage
+  ports:
+    - protocol: TCP
+      port: 3900
+      targetPort: 3900
+  clusterIP: None
diff --git a/manifests/migration.yaml b/manifests/migration.yaml
index 1c5b328..70ad541 100644
--- a/manifests/migration.yaml
+++ b/manifests/migration.yaml
@@ -13,7 +13,7 @@ spec:
     spec:
       restartPolicy: Never
       containers:
-        - image: ghcr.io/virtool/virtool:36.0.0
+        - image: ghcr.io/virtool/virtool:36.15.1
           name: virtool-migration
           command: ["virtool", "migration", "apply"]
           env:
diff --git a/manifests/ui/kustomization.yaml b/manifests/ui/kustomization.yaml
index f993652..90daec9 100644
--- a/manifests/ui/kustomization.yaml
+++ b/manifests/ui/kustomization.yaml
@@ -1,6 +1,6 @@
 images:
   - name: ghcr.io/virtool/ui
-    newTag: 7.5.2
+    newTag: 7.13.1
 
 labels:
   - pairs:
diff --git a/manifests/virtool/base/kustomization.yaml b/manifests/virtool/base/kustomization.yaml
index 1c3b5d3..d5682dc 100644
--- a/manifests/virtool/base/kustomization.yaml
+++ b/manifests/virtool/base/kustomization.yaml
@@ -1,6 +1,6 @@
 images:
   - name: ghcr.io/virtool/virtool
-    newTag: 36.0.0
+    newTag: 36.20.0
 
 labels:
   - pairs:
diff --git a/manifests/workflows/build-index.yaml b/manifests/workflows/build-index.yaml
index dc8c9ef..69a6a7e 100644
--- a/manifests/workflows/build-index.yaml
+++ b/manifests/workflows/build-index.yaml
@@ -14,12 +14,14 @@ spec:
       spec:
         containers:
           - name: workflow-build-index
-            image: ghcr.io/virtool/build-index:5.4.8
+            image: ghcr.io/virtool/build-index:5.7.0
             env:
               - name: VT_PROC
                 value: "2"
               - name: VT_MEM
                 value: "2"
+              - name: VT_WORKFLOW
+                value: build_index
             resources:
               limits:
                 cpu: 3
@@ -30,7 +32,7 @@ spec:
   triggers:
     - type: metrics-api
       metadata:
-        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/counts"
         valueLocation: "pending.build_index"
         targetValue: "1"
         activationTargetValue: "0"
diff --git a/manifests/workflows/create-sample.yaml b/manifests/workflows/create-sample.yaml
index 95024c3..cb84e16 100644
--- a/manifests/workflows/create-sample.yaml
+++ b/manifests/workflows/create-sample.yaml
@@ -14,12 +14,14 @@ spec:
       spec:
         containers:
           - name: workflow-create-sample
-            image: ghcr.io/virtool/create-sample:4.3.8
+            image: ghcr.io/virtool/create-sample:4.6.0
             env:
               - name: VT_PROC
                 value: "2"
               - name: VT_MEM
                 value: "4"
+              - name: VT_WORKFLOW
+                value: create_sample
             resources:
               limits:
                 cpu: 2700m
@@ -30,7 +32,7 @@ spec:
   triggers:
     - type: metrics-api
       metadata:
-        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/counts"
         valueLocation: "pending.create_sample"
         targetValue: "1"
         activationTargetValue: "0"
diff --git a/manifests/workflows/create-subtraction.yaml b/manifests/workflows/create-subtraction.yaml
index 399dafe..30287dc 100644
--- a/manifests/workflows/create-subtraction.yaml
+++ b/manifests/workflows/create-subtraction.yaml
@@ -14,12 +14,14 @@ spec:
       spec:
         containers:
           - name: workflow-create-subtraction
-            image: ghcr.io/virtool/create-subtraction:5.3.8
+            image: ghcr.io/virtool/create-subtraction:5.5.0
             env:
               - name: VT_PROC
                 value: "2"
               - name: VT_MEM
                 value: "2"
+              - name: VT_WORKFLOW
+                value: create_subtraction
             resources:
               limits:
                 cpu: "3"
@@ -30,7 +32,7 @@ spec:
   triggers:
     - type: metrics-api
       metadata:
-        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/counts"
         valueLocation: "pending.create_subtraction"
         targetValue: "1"
         activationTargetValue: "0"
diff --git a/manifests/workflows/iimi.yaml b/manifests/workflows/iimi.yaml
index f00de29..7e29c77 100644
--- a/manifests/workflows/iimi.yaml
+++ b/manifests/workflows/iimi.yaml
@@ -20,6 +20,8 @@ spec:
                 value: "4"
               - name: VT_PROC
                 value: "10"
+              - name: VT_WORKFLOW
+                value: iimi
             resources:
               limits:
                 cpu: "5"
@@ -30,7 +32,7 @@ spec:
   triggers:
     - type: metrics-api
       metadata:
-        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/counts"
         valueLocation: "pending.iimi"
         targetValue: "1"
         activationTargetValue: "0"
diff --git a/manifests/workflows/nuvs.yaml b/manifests/workflows/nuvs.yaml
index a96085b..8bccf79 100644
--- a/manifests/workflows/nuvs.yaml
+++ b/manifests/workflows/nuvs.yaml
@@ -11,12 +11,14 @@ spec:
       spec:
         containers:
           - name: workflow-nuvs
-            image: ghcr.io/virtool/nuvs:5.4.5
+            image: ghcr.io/virtool/nuvs:5.6.0
             env:
               - name: VT_PROC
                 value: "4"
               - name: VT_MEM
                 value: "10"
+              - name: VT_WORKFLOW
+                value: nuvs
             resources:
               limits:
                 cpu: "5"
@@ -27,7 +29,7 @@ spec:
   triggers:
     - type: metrics-api
       metadata:
-        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/counts"
         valueLocation: "pending.nuvs"
         targetValue: "1"
         activationTargetValue: "0"
diff --git a/manifests/workflows/pathoscope.yaml b/manifests/workflows/pathoscope.yaml
index 57747c2..172bd02 100644
--- a/manifests/workflows/pathoscope.yaml
+++ b/manifests/workflows/pathoscope.yaml
@@ -11,12 +11,14 @@ spec:
       spec:
         containers:
           - name: workflow-pathoscope
-            image: ghcr.io/virtool/pathoscope:5.9.4
+            image: ghcr.io/virtool/pathoscope:5.11.0
             env:
               - name: VT_MEM
                 value: "8"
               - name: VT_PROC
                 value: "4"
+              - name: VT_WORKFLOW
+                value: pathoscope
             resources:
               limits:
                 cpu: "5"
@@ -27,7 +29,7 @@ spec:
   triggers:
     - type: metrics-api
       metadata:
-        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/v2/counts"
+        url: "http://virtool-api-web-service.default.svc.cluster.local/jobs/counts"
         valueLocation: "pending.pathoscope"
         targetValue: "1"
         activationTargetValue: "0"

From f263bd98bfd59f73f6793117427c5c7251785f6b Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Thu, 30 Apr 2026 11:24:08 -0700
Subject: [PATCH 4/9] fix: update images

---
 Tiltfile                                  |  8 ++++++
 manifests/db/garage.yaml                  |  2 +-
 manifests/migration.yaml                  |  2 +-
 manifests/ui/kustomization.yaml           |  2 +-
 manifests/virtool/base/kustomization.yaml |  2 +-
 manifests/workflows/nuvs.yaml             |  2 +-
 manifests/workflows/pathoscope.yaml       |  2 +-
 scripts/pull.sh                           | 31 ++++++++++++++++-------
 scripts/wipe.sh                           | 23 +++++++++++++++++
 9 files changed, 59 insertions(+), 15 deletions(-)
 create mode 100644 scripts/wipe.sh

diff --git a/Tiltfile b/Tiltfile
index 07819a9..172b2a5 100644
--- a/Tiltfile
+++ b/Tiltfile
@@ -16,6 +16,14 @@ cmd_button('pull',
     text='Pull',
 )
 
+cmd_button('wipe',
+    argv=['bash', 'scripts/wipe.sh'],
+    icon_name="delete_forever",
+    location=location.NAV,
+    text='Wipe',
+    requires_confirmation=True,
+)
+
 helm_repo('kedacore', 'https://kedacore.github.io/charts', labels=['helm'])
 
 helm_resource(
diff --git a/manifests/db/garage.yaml b/manifests/db/garage.yaml
index d829350..cecd01b 100644
--- a/manifests/db/garage.yaml
+++ b/manifests/db/garage.yaml
@@ -30,7 +30,7 @@ data:
     #!/bin/sh
     set -eu
 
-    ADMIN_URL="http://garage:3903"
+    ADMIN_URL="http://127.0.0.1:3903"
     AUTH="Authorization: Bearer virtool-dev-admin-token"
     BUCKET="virtool"
     ACCESS_KEY_ID="GK000000000000000000000001"
diff --git a/manifests/migration.yaml b/manifests/migration.yaml
index 70ad541..e6aca7d 100644
--- a/manifests/migration.yaml
+++ b/manifests/migration.yaml
@@ -13,7 +13,7 @@ spec:
     spec:
       restartPolicy: Never
       containers:
-        - image: ghcr.io/virtool/virtool:36.15.1
+        - image: ghcr.io/virtool/virtool:36.24.0
           name: virtool-migration
           command: ["virtool", "migration", "apply"]
           env:
diff --git a/manifests/ui/kustomization.yaml b/manifests/ui/kustomization.yaml
index 90daec9..884d34a 100644
--- a/manifests/ui/kustomization.yaml
+++ b/manifests/ui/kustomization.yaml
@@ -1,6 +1,6 @@
 images:
   - name: ghcr.io/virtool/ui
-    newTag: 7.13.1
+    newTag: 7.13.3
 
 labels:
   - pairs:
diff --git a/manifests/virtool/base/kustomization.yaml b/manifests/virtool/base/kustomization.yaml
index d5682dc..0975e22 100644
--- a/manifests/virtool/base/kustomization.yaml
+++ b/manifests/virtool/base/kustomization.yaml
@@ -1,6 +1,6 @@
 images:
   - name: ghcr.io/virtool/virtool
-    newTag: 36.20.0
+    newTag: 36.24.0
 
 labels:
   - pairs:
diff --git a/manifests/workflows/nuvs.yaml b/manifests/workflows/nuvs.yaml
index 8bccf79..a93e15e 100644
--- a/manifests/workflows/nuvs.yaml
+++ b/manifests/workflows/nuvs.yaml
@@ -11,7 +11,7 @@ spec:
       spec:
         containers:
           - name: workflow-nuvs
-            image: ghcr.io/virtool/nuvs:5.6.0
+            image: ghcr.io/virtool/nuvs:5.7.0
             env:
               - name: VT_PROC
                 value: "4"
diff --git a/manifests/workflows/pathoscope.yaml b/manifests/workflows/pathoscope.yaml
index 172bd02..d40dc49 100644
--- a/manifests/workflows/pathoscope.yaml
+++ b/manifests/workflows/pathoscope.yaml
@@ -11,7 +11,7 @@ spec:
       spec:
         containers:
           - name: workflow-pathoscope
-            image: ghcr.io/virtool/pathoscope:5.11.0
+            image: ghcr.io/virtool/pathoscope:5.13.0
             env:
               - name: VT_MEM
                 value: "8"
diff --git a/scripts/pull.sh b/scripts/pull.sh
index ee13fca..2a0616d 100644
--- a/scripts/pull.sh
+++ b/scripts/pull.sh
@@ -6,18 +6,19 @@ if ! command -v jq &> /dev/null; then
     exit 1
 fi
 
-fetch_and_update() {
+fetch_latest_tag() {
     local repo=$1
-    local file=$2
-    local prefix=$3
-
-    # Fetch the latest release tag
     local url="https://api.github.com/repos/${repo}/releases/latest"
-    local tag=$(curl -s "$url" | jq -r '.tag_name')
+    curl -s "$url" | jq -r '.tag_name'
+}
+
+update_tag() {
+    local file=$1
+    local prefix=$2
+    local tag=$3
 
-    # Update the file if it exists
     if [[ -f "$file" ]]; then
-        sed -i "s/${prefix}[0-9.]\+/${prefix}${tag}/" "$file"
+        sed -i "s|${prefix}[0-9.]\+|${prefix}${tag}|" "$file"
         echo "Using tag '$tag' for $file"
     else
         echo "Error: File $file not found."
@@ -25,10 +26,22 @@ fetch_and_update() {
     fi
 }
 
+fetch_and_update() {
+    local repo=$1
+    local file=$2
+    local prefix=$3
+    local tag
+    tag=$(fetch_latest_tag "$repo")
+    update_tag "$file" "$prefix" "$tag"
+}
+
 echo "Server"
 echo ""
 
-fetch_and_update "virtool/virtool" "manifests/virtool/base/kustomization.yaml" "newTag: "
+virtool_tag=$(fetch_latest_tag "virtool/virtool")
+update_tag "manifests/virtool/base/kustomization.yaml" "newTag: " "$virtool_tag"
+update_tag "manifests/migration.yaml" "ghcr.io/virtool/virtool:" "$virtool_tag"
+
 fetch_and_update "virtool/virtool-ui" "manifests/ui/kustomization.yaml" "newTag: "
 
 echo ""
diff --git a/scripts/wipe.sh b/scripts/wipe.sh
new file mode 100644
index 0000000..9a8b3fc
--- /dev/null
+++ b/scripts/wipe.sh
@@ -0,0 +1,23 @@
+#!/bin/bash
+set -e
+
+echo "Deleting StatefulSets..."
+kubectl delete statefulset garage mongo postgres --ignore-not-found --wait=false
+
+echo "Deleting PVCs..."
+kubectl delete pvc \
+    data-garage-0 meta-garage-0 \
+    data-mongo-0 \
+    data-postgres-0 \
+    pvc-virtool \
+    --ignore-not-found --wait=false
+
+echo "Deleting PV..."
+kubectl delete pv pv-virtool --ignore-not-found --wait=false
+
+echo "Clearing host data at /virtool/data..."
+if [ -d /virtool/data ]; then
+    rm -rf /virtool/data/* 2>/dev/null || sudo rm -rf /virtool/data/*
+fi
+
+echo "Done. Tilt will recreate resources on next trigger."

From 9efbcd99e9417c82652d9788575fe836ea5f91d2 Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Thu, 30 Apr 2026 11:28:42 -0700
Subject: [PATCH 5/9] docs: add AGENTS.md and symlink CLAUDE.md to it

---
 AGENTS.md | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 CLAUDE.md |  1 +
 2 files changed, 69 insertions(+)
 create mode 100644 AGENTS.md
 create mode 120000 CLAUDE.md

diff --git a/AGENTS.md b/AGENTS.md
new file mode 100644
index 0000000..84ed1b6
--- /dev/null
+++ b/AGENTS.md
@@ -0,0 +1,68 @@
+# Dev
+
+This repository manages the local Kubernetes development environment for Virtool using Tilt and Minikube.
+
+## Stack
+
+- **Tilt** — orchestrates the dev cluster; the `Tiltfile` is the main entry point
+- **Minikube** — local Kubernetes cluster
+- **KEDA** — scales workflow jobs via a `metrics-api` trigger pointing at `http://virtool-api-web-service.../jobs/counts`
+- **MongoDB + PostgreSQL** — persisted across `tilt up`/`tilt down` runs via PVCs
+- **Garage** — self-hosted S3 store (replaces Redis); bootstrapped by an Alpine init-container that creates the `virtool` bucket and imports a dev access key
+
+## Layout
+
+```
+manifests/       Kustomize manifests for all cluster resources
+  db/            MongoDB, PostgreSQL, Garage
+  ingress.yaml
+  migration.yaml
+  storage.yaml
+  ui/
+  virtool/
+  workflows/     ScaledJob manifests for each workflow
+scripts/
+  init.sh        Create/reset the Minikube cluster
+  hosts.sh       Write cluster IP to /etc/hosts
+  pull.sh        Update image tags in kustomization + migration manifests
+  wipe.sh        Nuke PVCs, PVs, and host data
+Tiltfile         Tilt configuration (resources, buttons, live-edit flags)
+```
+
+## Common tasks
+
+**Start the cluster**
+```shell
+bash scripts/init.sh   # first time or full reset
+tilt up
+```
+
+**Live-edit a service** (repo must be a sibling of this directory)
+```shell
+tilt up -- --to-edit backend   # virtool/virtool
+tilt up -- --to-edit ui        # virtool/virtool-ui
+tilt up -- --to-edit <workflow-name>
+```
+
+Workflow names: `build-index`, `create-sample`, `create-subtraction`, `iimi`, `pathoscope`, `nuvs`
+
+**Update images**
+```shell
+bash scripts/pull.sh
+```
+Or click the **Pull** button in the Tilt UI.
+
+**Wipe persistent data**
+```shell
+bash scripts/wipe.sh
+```
+Or click the **Wipe** button in the Tilt UI (requires confirmation).
+
+**Update `/etc/hosts`** (needed once per cluster recreation)
+```shell
+bash scripts/hosts.sh
+```
+
+## PR guidelines
+
+- No test plan section in PR descriptions.
diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 120000
index 0000000..47dc3e3
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1 @@
+AGENTS.md
\ No newline at end of file

From 6ea1f212a55843867a443eefed04202208b7ee0f Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Fri, 1 May 2026 09:20:34 -0700
Subject: [PATCH 6/9] chore: harden dev scripts and refactor garage init

- scripts/wipe.sh: refuse to run unless kubectl current-context and
  the running Minikube profile are both 'virtool'; replace
  `sudo rm -rf /virtool/data/*` with `find -mindepth 1` so dotfiles
  are removed too.
- scripts/init.sh: pin every minikube/kubectl call to the dedicated
  'virtool' profile/context.
- scripts/pull.sh: strip leading 'v' from upstream tags and clean up
  the sed backup file.
- manifests/db/garage.yaml: move garage-init from an initContainer
  running apk-installed curl/jq to a sidecar using the
  badouralix/curl-jq image.
---
 manifests/db/garage.yaml | 34 +++++++++++++---------------------
 scripts/init.sh          | 22 ++++++++++++----------
 scripts/pull.sh          |  4 ++--
 scripts/wipe.sh          | 32 +++++++++++++++++++++++++-------
 4 files changed, 52 insertions(+), 40 deletions(-)

diff --git a/manifests/db/garage.yaml b/manifests/db/garage.yaml
index cecd01b..76fed28 100644
--- a/manifests/db/garage.yaml
+++ b/manifests/db/garage.yaml
@@ -36,8 +36,6 @@ data:
     ACCESS_KEY_ID="GK000000000000000000000001"
     SECRET_ACCESS_KEY="0000000000000000000000000000000000000000000000000000000000000001"
 
-    apk add --no-cache curl jq >/dev/null
-
     until curl -sf -H "${AUTH}" "${ADMIN_URL}/health" >/dev/null; do sleep 1; done
 
     NODE_ID=$(curl -sf -H "${AUTH}" "${ADMIN_URL}/v1/status" | jq -r '.node')
@@ -85,25 +83,6 @@ spec:
       labels:
         app: garage
     spec:
-      initContainers:
-        - name: garage-init
-          image: alpine:3.20
-          restartPolicy: Always
-          command: ["/bin/sh", "-c", "/scripts/init.sh && touch /tmp/ready && exec sleep infinity"]
-          resources:
-            requests:
-              cpu: 50m
-              memory: 32Mi
-            limits:
-              cpu: 100m
-              memory: 64Mi
-          readinessProbe:
-            exec:
-              command: ["test", "-f", "/tmp/ready"]
-            periodSeconds: 2
-          volumeMounts:
-            - name: init-script
-              mountPath: /scripts
       containers:
         - name: garage
           image: dxflrs/garage:v1.1.0
@@ -131,6 +110,19 @@ spec:
               mountPath: /var/lib/garage/meta
             - name: data
               mountPath: /var/lib/garage/data
+        - name: garage-init
+          image: badouralix/curl-jq
+          command: ["/bin/sh", "-c", "/scripts/init.sh && exec sleep infinity"]
+          resources:
+            requests:
+              cpu: 50m
+              memory: 32Mi
+            limits:
+              cpu: 100m
+              memory: 64Mi
+          volumeMounts:
+            - name: init-script
+              mountPath: /scripts
       volumes:
         - name: config
           configMap:
diff --git a/scripts/init.sh b/scripts/init.sh
index 6576874..aa90ca4 100644
--- a/scripts/init.sh
+++ b/scripts/init.sh
@@ -2,24 +2,26 @@
 
 set -e
 
-echo "Deleting any existing Minikube cluster..."
-minikube delete --purge=true
+PROFILE="virtool"
+
+echo "Deleting any existing Minikube cluster for profile '$PROFILE'..."
+minikube -p "$PROFILE" delete --purge=true
 
 echo "Starting Minikube for first time..."
-minikube start --cpus 8 --memory 16000
+minikube -p "$PROFILE" start --cpus 8 --memory 16000
 
 echo "Enabling Minikube addons..."
-minikube addons enable metrics-server
+minikube -p "$PROFILE" addons enable metrics-server
 
 echo "Generating TLS certificate for virtool.local..."
 CERT_DIR=$(mktemp -d)
 mkcert -key-file "$CERT_DIR/key.pem" -cert-file "$CERT_DIR/cert.pem" virtool.local
 
 echo "Creating TLS secrets..."
-kubectl -n kube-system create secret tls mkcert \
+kubectl --context "$PROFILE" -n kube-system create secret tls mkcert \
     --key "$CERT_DIR/key.pem" \
     --cert "$CERT_DIR/cert.pem"
-kubectl create secret tls mkcert \
+kubectl --context "$PROFILE" create secret tls mkcert \
     --key "$CERT_DIR/key.pem" \
     --cert "$CERT_DIR/cert.pem"
 
@@ -27,13 +29,13 @@ echo "Cleaning up temporary certificate files..."
 rm -rf "$CERT_DIR"
 
 echo "Configuring ingress addon to use custom certificate..."
-minikube addons configure ingress <<< "kube-system/mkcert"
-minikube addons enable ingress
+minikube -p "$PROFILE" addons configure ingress <<< "kube-system/mkcert"
+minikube -p "$PROFILE" addons enable ingress
 
 echo "Verifying ingress configuration..."
-kubectl -n ingress-nginx get deployment ingress-nginx-controller -o yaml | grep "kube-system"
+kubectl --context "$PROFILE" -n ingress-nginx get deployment ingress-nginx-controller -o yaml | grep "kube-system"
 
 echo "Configuring /etc/hosts..."
-MINIKUBE_IP=$(minikube ip)
+MINIKUBE_IP=$(minikube -p "$PROFILE" ip)
 sudo sed -i '/virtool.local/d' /etc/hosts
 echo -e "$MINIKUBE_IP\tvirtool.local" | sudo tee -a /etc/hosts
diff --git a/scripts/pull.sh b/scripts/pull.sh
index 2a0616d..4f483c5 100644
--- a/scripts/pull.sh
+++ b/scripts/pull.sh
@@ -9,7 +9,7 @@ fi
 fetch_latest_tag() {
     local repo=$1
     local url="https://api.github.com/repos/${repo}/releases/latest"
-    curl -s "$url" | jq -r '.tag_name'
+    curl -s "$url" | jq -r '.tag_name' | sed 's/^v//'
 }
 
 update_tag() {
@@ -18,7 +18,7 @@ update_tag() {
     local tag=$3
 
     if [[ -f "$file" ]]; then
-        sed -i "s|${prefix}[0-9.]\+|${prefix}${tag}|" "$file"
+        sed -i.bak "s|${prefix}[0-9.]\+|${prefix}${tag}|" "$file" && rm "${file}.bak"
         echo "Using tag '$tag' for $file"
     else
         echo "Error: File $file not found."
diff --git a/scripts/wipe.sh b/scripts/wipe.sh
index 9a8b3fc..3dce1a3 100644
--- a/scripts/wipe.sh
+++ b/scripts/wipe.sh
@@ -1,8 +1,28 @@
 #!/bin/bash
 set -e
 
+PROFILE="virtool"
+DATA_DIR="/virtool/data"
+
+current_context=$(kubectl config current-context 2>/dev/null || true)
+if [[ "$current_context" != "$PROFILE" ]]; then
+    echo "Refusing to wipe: kubectl current-context is '${current_context:-<none>}', expected '$PROFILE'."
+    echo "Switch contexts with: kubectl config use-context $PROFILE"
+    exit 1
+fi
+
+if ! minikube -p "$PROFILE" status >/dev/null 2>&1; then
+    echo "Refusing to wipe: Minikube profile '$PROFILE' is not running."
+    exit 1
+fi
+
+clear_data_dir() {
+    minikube -p "$PROFILE" ssh -- \
+        "test -d $DATA_DIR && sudo find $DATA_DIR -mindepth 1 -maxdepth 1 -exec rm -rf -- {} +"
+}
+
 echo "Deleting StatefulSets..."
-kubectl delete statefulset garage mongo postgres --ignore-not-found --wait=false
+kubectl delete statefulset garage mongo postgres --ignore-not-found
 
 echo "Deleting PVCs..."
 kubectl delete pvc \
@@ -10,14 +30,12 @@ kubectl delete pvc \
     data-mongo-0 \
     data-postgres-0 \
     pvc-virtool \
-    --ignore-not-found --wait=false
+    --ignore-not-found
 
 echo "Deleting PV..."
-kubectl delete pv pv-virtool --ignore-not-found --wait=false
+kubectl delete pv pv-virtool --ignore-not-found
 
-echo "Clearing host data at /virtool/data..."
-if [ -d /virtool/data ]; then
-    rm -rf /virtool/data/* 2>/dev/null || sudo rm -rf /virtool/data/*
-fi
+echo "Clearing contents of $DATA_DIR inside Minikube profile '$PROFILE'..."
+clear_data_dir
 
 echo "Done. Tilt will recreate resources on next trigger."

From 87baa40dc7d1b0a01cb4d9662e328cc46e043833 Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Fri, 1 May 2026 09:50:47 -0700
Subject: [PATCH 7/9] feat: replace garage with azurite

Swap the Garage S3 store for Azurite (the Azure Blob Storage emulator)
so the dev cluster matches the SDK and semantics used in production.

Drops the Garage StatefulSet, init sidecar, and admin/layout/key
bootstrap dance in favor of a single Azurite container with a /data
PVC. Updates Tiltfile, wipe.sh, and AGENTS.md to reference azurite.

App-side env wiring (connection string for devstoreaccount1) is a
follow-up in the virtool repo; the deployments in this repo do not
currently set any S3/Blob env vars.
---
 AGENTS.md                 |   4 +-
 Tiltfile                  |   6 +-
 manifests/db/azurite.yaml |  86 ++++++++++++++++++++
 manifests/db/garage.yaml  | 161 --------------------------------------
 scripts/wipe.sh           |   4 +-
 5 files changed, 93 insertions(+), 168 deletions(-)
 create mode 100644 manifests/db/azurite.yaml
 delete mode 100644 manifests/db/garage.yaml

diff --git a/AGENTS.md b/AGENTS.md
index 84ed1b6..1ee28f0 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -8,13 +8,13 @@ This repository manages the local Kubernetes development environment for Virtool
 - **Minikube** — local Kubernetes cluster
 - **KEDA** — scales workflow jobs via a `metrics-api` trigger pointing at `http://virtool-api-web-service.../jobs/counts`
 - **MongoDB + PostgreSQL** — persisted across `tilt up`/`tilt down` runs via PVCs
-- **Garage** — self-hosted S3 store (replaces Redis); bootstrapped by an Alpine init-container that creates the `virtool` bucket and imports a dev access key
+- **Azurite** — Azure Blob Storage emulator; uses the well-known dev account `devstoreaccount1` with key `Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==` and persists blobs at `/data` via a PVC
 
 ## Layout
 
 ```
 manifests/       Kustomize manifests for all cluster resources
-  db/            MongoDB, PostgreSQL, Garage
+  db/            MongoDB, PostgreSQL, Azurite
   ingress.yaml
   migration.yaml
   storage.yaml
diff --git a/Tiltfile b/Tiltfile
index 172b2a5..eaa7691 100644
--- a/Tiltfile
+++ b/Tiltfile
@@ -33,7 +33,7 @@ helm_resource(
     resource_deps=['kedacore']
 )
 
-k8s_yaml('manifests/db/garage.yaml')
+k8s_yaml('manifests/db/azurite.yaml')
 k8s_yaml('manifests/db/mongo.yaml')
 k8s_yaml('manifests/db/postgres.yaml')
 k8s_yaml('manifests/storage.yaml')
@@ -46,7 +46,7 @@ k8s_resource(
     labels=['data']
 )
 
-k8s_resource("garage", labels=['data'])
+k8s_resource("azurite", labels=['data'])
 k8s_resource("mongo", labels=['data'])
 k8s_resource("postgres", labels=['data'])
 
@@ -110,7 +110,7 @@ k8s_resource(
     'virtool-migration',
     labels=['virtool'],
     new_name="migration",
-    resource_deps=["garage", "mongo", "postgres", "storage"],
+    resource_deps=["azurite", "mongo", "postgres", "storage"],
     trigger_mode=TRIGGER_MODE_MANUAL
 )
 
diff --git a/manifests/db/azurite.yaml b/manifests/db/azurite.yaml
new file mode 100644
index 0000000..fde7fde
--- /dev/null
+++ b/manifests/db/azurite.yaml
@@ -0,0 +1,86 @@
+apiVersion: apps/v1
+kind: StatefulSet
+metadata:
+  name: azurite
+  labels:
+    app: azurite
+spec:
+  serviceName: azurite
+  replicas: 1
+  selector:
+    matchLabels:
+      app: azurite
+  template:
+    metadata:
+      labels:
+        app: azurite
+    spec:
+      containers:
+        - name: azurite
+          image: mcr.microsoft.com/azure-storage/azurite
+          args:
+            - azurite
+            - --blobHost
+            - 0.0.0.0
+            - --queueHost
+            - 0.0.0.0
+            - --tableHost
+            - 0.0.0.0
+            - --location
+            - /data
+          ports:
+            - containerPort: 10000
+              name: blob
+            - containerPort: 10001
+              name: queue
+            - containerPort: 10002
+              name: table
+          resources:
+            requests:
+              cpu: 100m
+              memory: 128Mi
+            limits:
+              cpu: 250m
+              memory: 256Mi
+          readinessProbe:
+            tcpSocket:
+              port: 10000
+            initialDelaySeconds: 2
+            periodSeconds: 5
+          livenessProbe:
+            tcpSocket:
+              port: 10000
+            initialDelaySeconds: 10
+            periodSeconds: 10
+          volumeMounts:
+            - name: data
+              mountPath: /data
+  volumeClaimTemplates:
+    - metadata:
+        name: data
+      spec:
+        accessModes: ["ReadWriteOnce"]
+        resources:
+          requests:
+            storage: 5Gi
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: azurite
+spec:
+  selector:
+    app: azurite
+  ports:
+    - name: blob
+      protocol: TCP
+      port: 10000
+      targetPort: 10000
+    - name: queue
+      protocol: TCP
+      port: 10001
+      targetPort: 10001
+    - name: table
+      protocol: TCP
+      port: 10002
+      targetPort: 10002
diff --git a/manifests/db/garage.yaml b/manifests/db/garage.yaml
deleted file mode 100644
index 76fed28..0000000
--- a/manifests/db/garage.yaml
+++ /dev/null
@@ -1,161 +0,0 @@
-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: garage-config
-data:
-  garage.toml: |
-    metadata_dir = "/var/lib/garage/meta"
-    data_dir = "/var/lib/garage/data"
-    db_engine = "sqlite"
-    replication_factor = 1
-    rpc_bind_addr = "[::]:3901"
-    rpc_public_addr = "garage:3901"
-    rpc_secret = "1111111111111111111111111111111111111111111111111111111111111111"
-
-    [s3_api]
-    s3_region = "garage"
-    api_bind_addr = "[::]:3900"
-    root_domain = ".s3.garage"
-
-    [admin]
-    api_bind_addr = "[::]:3903"
-    admin_token = "virtool-dev-admin-token"
----
-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: garage-init-script
-data:
-  init.sh: |
-    #!/bin/sh
-    set -eu
-
-    ADMIN_URL="http://127.0.0.1:3903"
-    AUTH="Authorization: Bearer virtool-dev-admin-token"
-    BUCKET="virtool"
-    ACCESS_KEY_ID="GK000000000000000000000001"
-    SECRET_ACCESS_KEY="0000000000000000000000000000000000000000000000000000000000000001"
-
-    until curl -sf -H "${AUTH}" "${ADMIN_URL}/health" >/dev/null; do sleep 1; done
-
-    NODE_ID=$(curl -sf -H "${AUTH}" "${ADMIN_URL}/v1/status" | jq -r '.node')
-    CURRENT_VERSION=$(curl -sf -H "${AUTH}" "${ADMIN_URL}/v1/layout" | jq -r '.version')
-
-    if [ "${CURRENT_VERSION}" = "0" ]; then
-      curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
-        -d "[{\"id\":\"${NODE_ID}\",\"zone\":\"dc1\",\"capacity\":1000000000,\"tags\":[]}]" \
-        "${ADMIN_URL}/v1/layout" >/dev/null
-      curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
-        -d '{"version":1}' "${ADMIN_URL}/v1/layout/apply" >/dev/null
-    fi
-
-    BUCKET_ID=$(curl -s -H "${AUTH}" "${ADMIN_URL}/v1/bucket?globalAlias=${BUCKET}" | jq -r '.id // empty')
-    if [ -z "${BUCKET_ID}" ]; then
-      BUCKET_ID=$(curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
-        -d "{\"globalAlias\":\"${BUCKET}\"}" "${ADMIN_URL}/v1/bucket" | jq -r '.id')
-    fi
-
-    EXISTING_KEY=$(curl -s -H "${AUTH}" "${ADMIN_URL}/v1/key?id=${ACCESS_KEY_ID}" | jq -r '.accessKeyId // empty')
-    if [ -z "${EXISTING_KEY}" ]; then
-      curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
-        -d "{\"accessKeyId\":\"${ACCESS_KEY_ID}\",\"secretAccessKey\":\"${SECRET_ACCESS_KEY}\",\"name\":\"virtool-dev-key\"}" \
-        "${ADMIN_URL}/v1/key/import" >/dev/null
-    fi
-
-    curl -sf -X POST -H "${AUTH}" -H "Content-Type: application/json" \
-      -d "{\"bucketId\":\"${BUCKET_ID}\",\"accessKeyId\":\"${ACCESS_KEY_ID}\",\"permissions\":{\"read\":true,\"write\":true,\"owner\":false}}" \
-      "${ADMIN_URL}/v1/bucket/allow" >/dev/null
-
-    echo "garage bootstrap ok: bucket=${BUCKET} key=${ACCESS_KEY_ID}"
----
-apiVersion: apps/v1
-kind: StatefulSet
-metadata:
-  name: garage
-spec:
-  serviceName: "garage"
-  replicas: 1
-  selector:
-    matchLabels:
-      app: garage
-  template:
-    metadata:
-      labels:
-        app: garage
-    spec:
-      containers:
-        - name: garage
-          image: dxflrs/garage:v1.1.0
-          ports:
-            - containerPort: 3900
-            - containerPort: 3903
-          resources:
-            requests:
-              cpu: 100m
-              memory: 128Mi
-            limits:
-              cpu: 250m
-              memory: 256Mi
-          readinessProbe:
-            httpGet:
-              path: /health
-              port: 3903
-            initialDelaySeconds: 2
-            periodSeconds: 5
-          volumeMounts:
-            - name: config
-              mountPath: /etc/garage.toml
-              subPath: garage.toml
-            - name: meta
-              mountPath: /var/lib/garage/meta
-            - name: data
-              mountPath: /var/lib/garage/data
-        - name: garage-init
-          image: badouralix/curl-jq
-          command: ["/bin/sh", "-c", "/scripts/init.sh && exec sleep infinity"]
-          resources:
-            requests:
-              cpu: 50m
-              memory: 32Mi
-            limits:
-              cpu: 100m
-              memory: 64Mi
-          volumeMounts:
-            - name: init-script
-              mountPath: /scripts
-      volumes:
-        - name: config
-          configMap:
-            name: garage-config
-        - name: init-script
-          configMap:
-            name: garage-init-script
-            defaultMode: 0755
-  volumeClaimTemplates:
-    - metadata:
-        name: meta
-      spec:
-        accessModes: ["ReadWriteOnce"]
-        resources:
-          requests:
-            storage: 1Gi
-    - metadata:
-        name: data
-      spec:
-        accessModes: ["ReadWriteOnce"]
-        resources:
-          requests:
-            storage: 5Gi
----
-apiVersion: v1
-kind: Service
-metadata:
-  name: garage
-spec:
-  selector:
-    app: garage
-  ports:
-    - protocol: TCP
-      port: 3900
-      targetPort: 3900
-  clusterIP: None
diff --git a/scripts/wipe.sh b/scripts/wipe.sh
index 3dce1a3..6b7d6e6 100644
--- a/scripts/wipe.sh
+++ b/scripts/wipe.sh
@@ -22,11 +22,11 @@ clear_data_dir() {
 }
 
 echo "Deleting StatefulSets..."
-kubectl delete statefulset garage mongo postgres --ignore-not-found
+kubectl delete statefulset azurite mongo postgres --ignore-not-found
 
 echo "Deleting PVCs..."
 kubectl delete pvc \
-    data-garage-0 meta-garage-0 \
+    data-azurite-0 \
     data-mongo-0 \
     data-postgres-0 \
     pvc-virtool \

From f518c8d5ac9336a41c044fd8a703e42e747d2d49 Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Fri, 1 May 2026 12:02:37 -0700
Subject: [PATCH 8/9] fix: fix azurite configuration

---
 manifests/db/azurite.yaml              | 28 ++++++++++++++++++++++++++
 manifests/virtool/base/deployment.yaml | 10 +++++++++
 2 files changed, 38 insertions(+)

diff --git a/manifests/db/azurite.yaml b/manifests/db/azurite.yaml
index fde7fde..70bb02c 100644
--- a/manifests/db/azurite.yaml
+++ b/manifests/db/azurite.yaml
@@ -15,6 +15,32 @@ spec:
       labels:
         app: azurite
     spec:
+      initContainers:
+        - name: azurite-init
+          image: mcr.microsoft.com/azure-cli:latest
+          restartPolicy: Always
+          env:
+            - name: AZURE_STORAGE_CONNECTION_STRING
+              value: "DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://127.0.0.1:10000/devstoreaccount1;"
+          command:
+            - /bin/sh
+            - -c
+            - |
+              set -eu
+              until az storage container create --name virtool --output none 2>/dev/null; do sleep 2; done
+              touch /tmp/ready
+              exec sleep infinity
+          resources:
+            requests:
+              cpu: 50m
+              memory: 64Mi
+            limits:
+              cpu: 200m
+              memory: 256Mi
+          readinessProbe:
+            exec:
+              command: ["test", "-f", "/tmp/ready"]
+            periodSeconds: 2
       containers:
         - name: azurite
           image: mcr.microsoft.com/azure-storage/azurite
@@ -28,6 +54,8 @@ spec:
             - 0.0.0.0
             - --location
             - /data
+            - --skipApiVersionCheck
+            - --disableProductStyleUrl
           ports:
             - containerPort: 10000
               name: blob
diff --git a/manifests/virtool/base/deployment.yaml b/manifests/virtool/base/deployment.yaml
index 7918a7f..03e288c 100644
--- a/manifests/virtool/base/deployment.yaml
+++ b/manifests/virtool/base/deployment.yaml
@@ -23,6 +23,16 @@ spec:
               value: "mongodb://virtool:virtool@mongo.default.svc.cluster.local/virtool"
             - name: VT_POSTGRES_CONNECTION_STRING
               value: "postgresql+asyncpg://virtool@postgres.default.svc.cluster.local?password=virtool"
+            - name: VT_STORAGE_BACKEND
+              value: "azure"
+            - name: VT_STORAGE_AZURE_ACCOUNT
+              value: "devstoreaccount1"
+            - name: VT_STORAGE_AZURE_CONTAINER
+              value: "virtool"
+            - name: VT_STORAGE_AZURE_ACCESS_KEY
+              value: "Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw=="
+            - name: VT_STORAGE_AZURE_ENDPOINT
+              value: "http://azurite.default.svc.cluster.local:10000/devstoreaccount1"
           ports:
             - containerPort: 9950
               protocol: TCP

From 8dd02086d40f99e50bd6ab3ceb5f39e959dad6e8 Mon Sep 17 00:00:00 2001
From: Ian Boyes <igboyes@gmail.com>
Date: Wed, 6 May 2026 09:02:27 -0700
Subject: [PATCH 9/9] fix: fix init and wipe scripts

---
 manifests/migration.yaml                  |  2 +-
 manifests/virtool/base/kustomization.yaml |  2 +-
 manifests/workflows/iimi.yaml             |  2 +-
 scripts/init.sh                           | 22 ++++++++++------------
 scripts/wipe.sh                           | 15 +++++++--------
 5 files changed, 20 insertions(+), 23 deletions(-)

diff --git a/manifests/migration.yaml b/manifests/migration.yaml
index e6aca7d..67c8044 100644
--- a/manifests/migration.yaml
+++ b/manifests/migration.yaml
@@ -13,7 +13,7 @@ spec:
     spec:
       restartPolicy: Never
       containers:
-        - image: ghcr.io/virtool/virtool:36.24.0
+        - image: ghcr.io/virtool/virtool:36.25.3
           name: virtool-migration
           command: ["virtool", "migration", "apply"]
           env:
diff --git a/manifests/virtool/base/kustomization.yaml b/manifests/virtool/base/kustomization.yaml
index 0975e22..55ef2df 100644
--- a/manifests/virtool/base/kustomization.yaml
+++ b/manifests/virtool/base/kustomization.yaml
@@ -1,6 +1,6 @@
 images:
   - name: ghcr.io/virtool/virtool
-    newTag: 36.24.0
+    newTag: 36.25.3
 
 labels:
   - pairs:
diff --git a/manifests/workflows/iimi.yaml b/manifests/workflows/iimi.yaml
index 7e29c77..c698e52 100644
--- a/manifests/workflows/iimi.yaml
+++ b/manifests/workflows/iimi.yaml
@@ -14,7 +14,7 @@ spec:
       spec:
         containers:
           - name: virtool-workflow
-            image: ghcr.io/virtool/iimi:0.4.5
+            image: ghcr.io/virtool/iimi:0.5.0
             env:
               - name: VT_MEM
                 value: "4"
diff --git a/scripts/init.sh b/scripts/init.sh
index aa90ca4..6576874 100644
--- a/scripts/init.sh
+++ b/scripts/init.sh
@@ -2,26 +2,24 @@
 
 set -e
 
-PROFILE="virtool"
-
-echo "Deleting any existing Minikube cluster for profile '$PROFILE'..."
-minikube -p "$PROFILE" delete --purge=true
+echo "Deleting any existing Minikube cluster..."
+minikube delete --purge=true
 
 echo "Starting Minikube for first time..."
-minikube -p "$PROFILE" start --cpus 8 --memory 16000
+minikube start --cpus 8 --memory 16000
 
 echo "Enabling Minikube addons..."
-minikube -p "$PROFILE" addons enable metrics-server
+minikube addons enable metrics-server
 
 echo "Generating TLS certificate for virtool.local..."
 CERT_DIR=$(mktemp -d)
 mkcert -key-file "$CERT_DIR/key.pem" -cert-file "$CERT_DIR/cert.pem" virtool.local
 
 echo "Creating TLS secrets..."
-kubectl --context "$PROFILE" -n kube-system create secret tls mkcert \
+kubectl -n kube-system create secret tls mkcert \
     --key "$CERT_DIR/key.pem" \
     --cert "$CERT_DIR/cert.pem"
-kubectl --context "$PROFILE" create secret tls mkcert \
+kubectl create secret tls mkcert \
     --key "$CERT_DIR/key.pem" \
     --cert "$CERT_DIR/cert.pem"
 
@@ -29,13 +27,13 @@ echo "Cleaning up temporary certificate files..."
 rm -rf "$CERT_DIR"
 
 echo "Configuring ingress addon to use custom certificate..."
-minikube -p "$PROFILE" addons configure ingress <<< "kube-system/mkcert"
-minikube -p "$PROFILE" addons enable ingress
+minikube addons configure ingress <<< "kube-system/mkcert"
+minikube addons enable ingress
 
 echo "Verifying ingress configuration..."
-kubectl --context "$PROFILE" -n ingress-nginx get deployment ingress-nginx-controller -o yaml | grep "kube-system"
+kubectl -n ingress-nginx get deployment ingress-nginx-controller -o yaml | grep "kube-system"
 
 echo "Configuring /etc/hosts..."
-MINIKUBE_IP=$(minikube -p "$PROFILE" ip)
+MINIKUBE_IP=$(minikube ip)
 sudo sed -i '/virtool.local/d' /etc/hosts
 echo -e "$MINIKUBE_IP\tvirtool.local" | sudo tee -a /etc/hosts
diff --git a/scripts/wipe.sh b/scripts/wipe.sh
index 6b7d6e6..0f67014 100644
--- a/scripts/wipe.sh
+++ b/scripts/wipe.sh
@@ -1,23 +1,22 @@
 #!/bin/bash
 set -e
 
-PROFILE="virtool"
 DATA_DIR="/virtool/data"
 
 current_context=$(kubectl config current-context 2>/dev/null || true)
-if [[ "$current_context" != "$PROFILE" ]]; then
-    echo "Refusing to wipe: kubectl current-context is '${current_context:-<none>}', expected '$PROFILE'."
-    echo "Switch contexts with: kubectl config use-context $PROFILE"
+if [[ "$current_context" != "minikube" ]]; then
+    echo "Refusing to wipe: kubectl current-context is '${current_context:-<none>}', expected 'minikube'."
+    echo "Switch contexts with: kubectl config use-context minikube"
     exit 1
 fi
 
-if ! minikube -p "$PROFILE" status >/dev/null 2>&1; then
-    echo "Refusing to wipe: Minikube profile '$PROFILE' is not running."
+if ! minikube status >/dev/null 2>&1; then
+    echo "Refusing to wipe: Minikube is not running."
     exit 1
 fi
 
 clear_data_dir() {
-    minikube -p "$PROFILE" ssh -- \
+    minikube ssh -- \
         "test -d $DATA_DIR && sudo find $DATA_DIR -mindepth 1 -maxdepth 1 -exec rm -rf -- {} +"
 }
 
@@ -35,7 +34,7 @@ kubectl delete pvc \
 echo "Deleting PV..."
 kubectl delete pv pv-virtool --ignore-not-found
 
-echo "Clearing contents of $DATA_DIR inside Minikube profile '$PROFILE'..."
+echo "Clearing contents of $DATA_DIR..."
 clear_data_dir
 
 echo "Done. Tilt will recreate resources on next trigger."