Tweaks for actual run and s3 manipulation

.gitignore

+pdbfix/fixed_pdbs/

pdbfix/pdbfix_sample_jm_pushbucket.yaml

+apiVersion: v1
+kind: Pod
+metadata:
+  name: pdbscan-jm-pushbucket
+spec:
+  containers:
+    - name: pdbscan-jm-rclone
+      image: rclone/rclone
+      resources:
+        limits:
+          memory: 100Mi
+          cpu: 100m
+        requests:
+          memory: 100Mi
+          cpu: 100m
+      command:
+        [
+          "rclone",
+          "--config=/secrets/rclone.conf",
+          "copy",
+          "/opt/fixed_pdbs",
+          "nrp-internal:fixed-pdbs-bucket/files",
+        ]
+      volumeMounts:
+        - mountPath: /opt/fixed_pdbs
+          name: fixed-pdbs
+        - name: rclone-config
+          mountPath: /secrets/rclone.conf
+          subPath: rclone.conf
+  volumes:
+    - name: fixed-pdbs
+      persistentVolumeClaim:
+        claimName: pdbscan-jm-workerpvc
+    - name: rclone-config
+      secret:
+        secretName: jm-rclone-config

pdbfix/pdbfix_sample_jm_pvc.yaml

@@ -8,4 +8,4 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-      storage: 1Gi
+      storage: 10Gi

pdbfix/pdbfix_sample_jm_worker.yaml

@@ -16,7 +16,7 @@ spec:
                     values:
                       - "true"
       priorityClassName: opportunistic
-      restartPolicy: Never
+      restartPolicy: OnFailure
       initContainers:
         - name: pdbscan-jm-init-git
           image: alpine/git
@@ -57,10 +57,10 @@ spec:
           image: gitlab-registry.nrp-nautilus.io/josh.mitchell/pdb-census:latest
           resources:
             limits:
-              memory: "2Gi"
+              memory: "5Gi"
               cpu: "1"
             requests:
-              memory: "2Gi"
+              memory: "5Gi"
               cpu: "1"
           command:
             - micromamba