Merge branch 'main' into tclabby-main-patch-29326

content/3.defense-systems/butters_gp57r.md

@@ -12,7 +12,13 @@ relevantAbstracts:
 
 # Butters_gp57r
 
-## To do 
+## Description
+
+The Butters_gp57r system is encoded in the Butters mycobacterium prophage and has been shown to inhibit rival phage replication [YP_009304936.1](https://ncbi.nlm.nih.gov/protein/YP_009304936.1).
+
+## Molecular Mechanism
+
+Butters_gp57r is activated post-DNA injeciton and inhibits island3 and other phage DNA amplification. This system may inhibit heterotypic phage infeciton with the HEPN domain [YP_009304936.1](https://ncbi.nlm.nih.gov/protein/YP_009304936.1). 
 
 ## Example of genomic structure
 

deploy/df-wiki/templates/deployment.yaml

@@ -29,6 +29,14 @@ spec:
       serviceAccountName: {{ include "df-wiki.serviceAccountName" . }}
       securityContext:
         {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      initContainers:
+        - name: init-directory
+          image: busybox
+          command: ["/bin/sh", "-c"]
+          args: ["mkdir -p /struct/wiki", chown -R 101:101 /struct/wiki"]
+          volumeMounts:
+            - name: structure-data-pvc
+              mountPath: /struct
       containers:
         - name: {{ .Chart.Name }}
           securityContext:
@@ -39,23 +47,24 @@ spec:
             - name: http
               containerPort: {{ .Values.service.port }}
               protocol: TCP
-          livenessProbe:
-            httpGet:
-              path: /wiki/
-              port: http
-          readinessProbe:
-            httpGet:
-              path: /wiki/
-              port: http
+          # livenessProbe:
+          #   httpGet:
+          #     path: /
+          #     port: http
+          # readinessProbe:
+          #   httpGet:
+          #     path: /
+          #     port: http
           resources:
             {{- toYaml .Values.resources | nindent 12 }}
           volumeMounts:
           - mountPath: /tmp
             name: tmp
           - name: nginx-config
-            mountPath: /etc/nginx/conf.d/
+            mountPath: /etc/nginx/conf.d
           - name: structure-data-pvc
             mountPath: /usr/share/nginx/html
+            subPath: wiki
           - name: website-pvc
             mountPath: /website
           

deploy/df-wiki/templates/pvc-structure.yaml

@@ -10,5 +10,5 @@ spec:
   resources:
     requests:
       storage: 35Gi
-  storageClassName: isilon
+  storageClassName: ceph-fs
   volumeMode: Filesystem
\ No newline at end of file

deploy/df-wiki/templates/pvc-website.yaml

@@ -10,6 +10,5 @@ spec:
   resources:
     requests:
       storage: 800Mi
-  # storageClassName: {{ .Values.storageClassName }}
-  storageClassName: isilon
+  storageClassName: ceph-fs
   volumeMode: Filesystem
\ No newline at end of file

deploy/df-wiki/values.development.yaml

@@ -23,6 +23,3 @@ resources:
 
 autoscaling:
   enabled: false
-
-
-storageClassName: isilon
\ No newline at end of file

deploy/df-wiki/values.yaml

@@ -28,8 +28,7 @@ serviceAccount:
 podAnnotations: {}
 
 podSecurityContext:
-  {}
-  # fsGroup: 2000
+  fsGroup: 101
 
 securityContext:
   runAsNonRoot: true

deploy/meilisearch/values.development.yaml

@@ -8,7 +8,7 @@ meilisearch:
       nginx.ingress.kubernetes.io/proxy-body-size: 100m
   persistence:
     enabled: true
-    storageClass: isilon
+    storageClass: ceph-block
     size: "4Gi"
   resources: 
     limits: