diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index 7436a068..9fe495e6 100644
--- a/.github/workflows/packaging.yml
+++ b/.github/workflows/packaging.yml
@@ -20,7 +20,7 @@ jobs:
     name: Package and push from PR
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
            persist-credentials: false
       - uses: cloudve/helm-ci@master
@@ -36,7 +36,7 @@ jobs:
     name: Package and push manual invocation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
            persist-credentials: false
       - uses: cloudve/helm-ci@master
@@ -51,13 +51,20 @@ jobs:
     needs: [ package-from-pr, package-from-manual ]
     name: Create a tag and GitHub release for this version.
     runs-on: ubuntu-latest
+    env:
+      GH_TOKEN: ${{ github.token }}
     if: |
       always() 
       && contains(needs.*.result, 'success')
       && !contains(needs.*.result, 'failure')
     steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.ref }}
       - name: Tag and release
         run: |
+          git config user.name "GitHub Actions Bot"
+          git config user.email "<>"
           version=v$(cat galaxy/Chart.yaml | grep ^version: | awk '{print $2}')
           git tag -a $version -m "Automatic release of $version"
           git push origin $version
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index bbde0299..db7f47f9 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -34,7 +34,7 @@ jobs:
       - name: Start k8s locally
         uses: jupyterhub/action-k3s-helm@v3
         with:
-          k3s-version: v1.25.15+k3s2  # releases:  https://github.com/k3s-io/k3s/tags
+          k3s-version: v1.28.7+k3s1  # releases:  https://github.com/k3s-io/k3s/tags
           metrics-enabled: false
           traefik-enabled: false
       - name: Verify function of k8s, kubectl, and helm
@@ -64,3 +64,17 @@ jobs:
       - name: Print workflow handler log
         run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-workflow[^ ]*')"
         if: always()
+      - name: Check appVersion
+        if: always()
+        run: |
+          kubectl get svc -n galaxy
+          kubectl describe svc -n galaxy galaxy-nginx
+          appVersion=$(cat galaxy/Chart.yaml | grep ^appVersion: | awk '{print $2}' | tr -d '"')
+          address=$(kubectl get svc -n galaxy galaxy-nginx -o jsonpath="http://{.spec.clusterIP}:{.spec.ports[0].port}/galaxy/api/version")
+          echo "Address is $address"
+          apiVersion=$(curl $address | jq -r '"\(.version_major).\(.version_minor)"')
+          echo "appVersion: $appVersion"          
+          echo "apiVersion: $apiVersion"
+          if [ "$appVersion" != "$apiVersion" ]; then
+            exit 1
+          fi  
diff --git a/README.md b/README.md
index f7684f85..fc7d6871 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Galaxy Helm Chart (v4)
+# Galaxy Helm Chart (v5)
 
 [Galaxy](https://galaxyproject.org/) is a data analysis platform focusing on
 accessibility, reproducibility, and transparency of primarily bioinformatics
@@ -8,7 +8,7 @@ updates, upgrades, and rollbacks.
 
 ## Supported software versions
 
-- Kubernetes 1.22+
+- Kubernetes 1.27+
 - Helm 3.5+
 
 ## Kubernetes cluster
@@ -272,6 +272,8 @@ jobHandlers:
     failureThreshhold: 3
 ```
 
+# Additional Configurations
+
 ## Extra File Mappings
 
 The `extraFileMappings` field can be used to inject files to arbitrary paths in the `nginx` deployment, as well as any of the `job`, `web`, or `workflow` handlers, and the `init` jobs.
@@ -393,6 +395,9 @@ wildcard DNS mapping to `*.its.<host_name>`. To make Interactive Tools work on
 localhost, you can use `dnsmasq` or similar to handle wildcard DNS mappings for
 `*.localhost`.
 
+For linux:
+Follow the instructions here to configure dnsmasq on Linux: https://superuser.com/a/1718296
+
 For mac:
 ```bash
   $ brew install dnsmasq
@@ -420,28 +425,76 @@ The Galaxy application can be horizontally scaled for the web, job, or workflow
 by setting the desired values of the `webHandlers.replicaCount`,
 `jobHandlers.replicaCount`, and `workflowHandlers.replicaCount` configuration options.
 
-## Galaxy versions
+## Cron jobs
+
+Two Cron jobs are defined by default.  One to clean up Galaxy's database and one to clean up the `tmp` directory.  By default, these
+jobs run at 02:05 (the database maintenance script) and 02:15 (`tmp` directyory cleanup). Users can 
+change the times the cron jobs are run by changing the `schedule` field in the `values.yaml` file:
+
+```yaml
+cronJobs:
+  maintenance:
+    schedule: "30 6 * * *" # Execute the cron job at 6:30 UTC
+```
+or by specifying the `schedule` on the command line when instaling Galaxy:
+```bash
+# Schedule the maintenance job to run at 06:30 on the first day of each month
+helm install galaxy -n galaxy galaxy/galaxy --set cronJobs.maintenance.schedule="30 6 1 * *"
+```
+To disable a cron job after Galaxy has been deployed simply set the enabled flag for that job to false:
+
+
+```bash
+helm upgrade galaxy -n galaxy galaxy/galaxy --reuse-values --set cronJobs.maintenance.enabled=false
+```
 
-Some changes introduced in the chart sometimes rely on changes in the Galaxy
-container image, especially in relation to the Kubernetes runner. This table
-keeps track of recommended Chart versions for particular Galaxy versions as
-breaking changes are introduced. Otherwise, the Galaxy image and chart should be
-independently upgrade-able. In other words, upgrading the Galaxy image from
-`21.05` to `21.09` should be a matter of `helm upgrade my-galaxy cloudve/galaxy
---reuse-values --set image.tag=21.09`.
+### Run a CronJob manually
+
+Cron jobs can be invoked manually with tools such as [OpenLens](https://github.com/MuhammedKalkan/OpenLens)
+or from the command line with `kubectl`
+```bash
+kubectl create job --namespace <namespace> <job name> --from cronjob/galaxy-cron-maintenance 
+```
+This will run the cron job regardless of the `schedule` that has been set.
+
+**Note:** the name of the cron job will be `{{ .Release.Name }}-cron-<job name>` where the `<job name>`
+is the name (key) used in the `values.yaml` file.
+
+### CronJob configuration
+
+The following fields can be specified when defining cron jobs.
+
+| Name | Definition                                                                                                                                | Required |
+|---|-------------------------------------------------------------------------------------------------------------------------------------------|----------|
+| enabled | `true` or `false`.  If `false` the cron job will not be run.  Default is `true` | **Yes**  |
+| schedule | When the job will be run.  Use tools such as [crontab.guru](https://crontab.guru) for assistance determining the proper schedule string   | **Yes**  |
+| defaultEnv | `true` or `false`. See the `galaxy.podEnvVars` macro in `_helpers.tpl` for the list of variables that will be defined. Default is `false` | No       |
+| extraEnv | Define extra environment variables that will be available to the job | No       |
+| securityContext | Specifies a `securityContext` for the job. Typically used to set `runAsUser` | No       |
+| image | Specify the Docker container used to run the job | No       |
+| command | The command to run | **Yes**  |
+| args | Any command line arguments that should be passed to the `command` | No       |
+| extraFileMappings | Allow arbitrary files to be mounted from config maps | No       |
+
+### Notes
+
+If specifying the Docker `image` both the `resposity` and `tag` MUST be specified.
+```yaml
+  image:
+    repository: quay.io/my-organization/my-image
+    tag: "1.0"  
+```
 
+The `extraFileMappings` block is similar to the global `extraFileMappings` except the file will only be mounted for that cron job.
+The following fields can be specified for each file.
 
-| Chart version        | Galaxy version   | Description     |
-| :------------------ | :--------------- | :-------------- |
-| `5.0`               | `22.05`          | Needs at least container image 22.05 as Galaxy switched from uwsgi to gunicorn  |
-| `4.0`               | `21.05`          | Needs [Galaxy PR#11899](https://github.com/galaxyproject/galaxy/pull/11899) for eliminating the CVMFS. If running chart 4.0+ with Galaxy image `21.01` or below, use the CVMFS instead with `--set setupJob.downloadToolConfs.enabled=false --set cvmfs.repositories.cvmfs-gxy-cloud=cloud.galaxyproject.org --set cvmfs.galaxyPersistentVolumeClaims.cloud.storage=1Gi --set cvmfs.galaxyPersistentVolumeClaims.cloud.storageClassName=cvmfs-gxy-cloud --set cvmfs.galaxyPersistentVolumeClaims.cloud.mountPath=/cvmfs/cloud.galaxyproject.org` |
+| Name | Definition | Required |
+|---|---|----------|
+| mode | The file mode (permissions) assigned to the file | No       |
+| tpl | If set to `true` the file contents will be run through Helm's templating engine. Defaults to `false` | No       |
+| content | The contents of the file | **Yes**  | 
 
-## Funding
 
-- _Version 3+_: Galaxy Project, Genomics Virtual Laboratory (GVL)
+See the `example` cron job included in the `values.yaml` file for a full example.
 
-- _Version 2_: Genomics Virtual Laboratory (GVL), Galaxy Project, and European
-  Commission (EC) H2020 Project PhenoMeNal, grant agreement number 654241.
 
-- _Version 1_: European Commission (EC) H2020 Project PhenoMeNal, grant
-  agreement number 654241.
diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 870874b4..4c9252f5 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,8 +1,8 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.9.0-anvil.1
-appVersion: "24.0"
+version: 5.15.0-anvil.0
+appVersion: "24.1.1"
 description: Chart for Galaxy, an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
 icon: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png
 dependencies:
@@ -22,7 +22,7 @@ dependencies:
       - deploy-s3csi
   - name: galaxy-cvmfs-csi
     repository: https://raw.githubusercontent.com/cloudve/helm-charts/master/
-    version: 2.2.0
+    version: 2.4.0
     condition: cvmfs.deploy
     alias: cvmfs
     tags:
diff --git a/galaxy/disabled/configmap-galaxy.yaml b/galaxy/disabled/configmap-galaxy.yaml
new file mode 100644
index 00000000..6f49a14c
--- /dev/null
+++ b/galaxy/disabled/configmap-galaxy.yaml
@@ -0,0 +1,9 @@
+apiVersion: v1
+metadata:
+  name: {{ .Release.Name }}-galaxy-config
+  labels:
+    {{- include "galaxy.labels" $ | nindent 4 }}
+kind: ConfigMap
+data:
+  galaxy.yml: |
+    {{- .Values.galaxy | toYaml | nindent 4 }}
diff --git a/galaxy/files/configs/tool_conf.xml b/galaxy/files/configs/tool_conf.xml
index 6870427f..381ab817 100644
--- a/galaxy/files/configs/tool_conf.xml
+++ b/galaxy/files/configs/tool_conf.xml
@@ -38,6 +38,10 @@
     <tool file="${model_tools_path}/build_list.xml" />
     <tool file="${model_tools_path}/extract_dataset.xml" />
   </section>
+  <section id="expression_tools" name="Expression Tools">
+    <tool file="expression_tools/parse_values_from_file.xml"/>
+    <tool file="expression_tools/pick_value.xml"/>
+  </section>
   <label id="general_text_label" text="General Text Tools" />
   <section id="text_manipulation" name="Text Manipulation">
     <tool file="filters/fixedValueColumn.xml" />
diff --git a/galaxy/templates/_helpers.tpl b/galaxy/templates/_helpers.tpl
index 7e0df8f6..3472705d 100644
--- a/galaxy/templates/_helpers.tpl
+++ b/galaxy/templates/_helpers.tpl
@@ -83,6 +83,13 @@ postgresql.fullname string and then prepend the release name to form the service
 {{- end -}}
 {{- end -}}
 
+{{/*
+Generate the connection string needed to connect to a Postres database
+*/}}
+{{- define "galaxy-postgresql.connection-string" -}}
+{{- printf "postgresql://%s:%s@%s/galaxy%s" .Values.postgresql.galaxyDatabaseUser (include "galaxy.galaxyDbPassword" .) (include "galaxy-postgresql.fullname" .) .Values.postgresql.galaxyConnectionParams -}}
+{{- end -}}
+
 {{/*
 Return the rabbitmq cluster to use
 */}}
diff --git a/galaxy/templates/configmap-cvmfs-fix.yaml b/galaxy/templates/configmap-cvmfs-fix.yaml
index d5d4c129..f680f119 100644
--- a/galaxy/templates/configmap-cvmfs-fix.yaml
+++ b/galaxy/templates/configmap-cvmfs-fix.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 kind: ConfigMap
 metadata:
diff --git a/galaxy/templates/configmap-extra-files.yaml b/galaxy/templates/configmap-extra-files.yaml
index b0e60f60..53dc516c 100644
--- a/galaxy/templates/configmap-extra-files.yaml
+++ b/galaxy/templates/configmap-extra-files.yaml
@@ -1,5 +1,6 @@
 {{- range $key, $entry := .Values.extraFileMappings -}}
 {{- if $entry }}
+---
 apiVersion: v1
 metadata:
   # Extract the filename portion only
@@ -20,9 +21,9 @@ data:
   {{- else }}
     {{- $entry.content | nindent 4 }}
   {{- end }}
----
 {{- end }}
 {{- end }}
+---
 apiVersion: v1
 metadata:
   name: {{ include "galaxy.fullname" $ }}-probedb-py
@@ -32,5 +33,3 @@ kind: ConfigMap
 data:
   probedb.py: |
     {{- (.Files.Get "scripts/probedb.py") | nindent 4 }}
-
----
diff --git a/galaxy/templates/configmap-galaxy-rules.yaml b/galaxy/templates/configmap-galaxy-rules.yaml
index aaa5101c..ed09bb95 100644
--- a/galaxy/templates/configmap-galaxy-rules.yaml
+++ b/galaxy/templates/configmap-galaxy-rules.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 kind: ConfigMap
 metadata:
diff --git a/galaxy/templates/configmap-grafana-dashboard.yaml b/galaxy/templates/configmap-grafana-dashboard.yaml
index 58d573aa..1ced09bb 100644
--- a/galaxy/templates/configmap-grafana-dashboard.yaml
+++ b/galaxy/templates/configmap-grafana-dashboard.yaml
@@ -1,4 +1,5 @@
 {{- if .Values.influxdb.enabled }}
+---
 apiVersion: v1
 kind: ConfigMap
 metadata:
diff --git a/galaxy/templates/configmap-nginx.yaml b/galaxy/templates/configmap-nginx.yaml
index d1166b32..a74409cd 100644
--- a/galaxy/templates/configmap-nginx.yaml
+++ b/galaxy/templates/configmap-nginx.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 kind: ConfigMap
 metadata:
diff --git a/galaxy/templates/configs-galaxy.yaml b/galaxy/templates/configs-galaxy.yaml
index f1b0e229..4fa8a7ec 100644
--- a/galaxy/templates/configs-galaxy.yaml
+++ b/galaxy/templates/configs-galaxy.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 metadata:
   name: {{ include "galaxy.fullname" . }}-configs
diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 17b0219a..d020b4f7 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,47 +1,118 @@
+{{ range $key, $cronjob := .Values.cronJobs }}
+---
 apiVersion: batch/v1
 kind: CronJob
 metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance
+  name: {{ include "galaxy.fullname" $ }}-cron-{{ $key }}
   labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
+    {{- include "galaxy.labels" $ | nindent 4 }}
 spec:
-  schedule: "0 2 * * *"
+  {{- if $cronjob.enabled }}
+  schedule: {{ $cronjob.schedule | quote }}
+  {{- else }}
+  # Set an impossible date so that the cronjob is still defined, but effectively disabled. 
+  #  This will allow the cronjob to be run manually if needed.
+  schedule: "0 0 30 2 *"
+  {{- end }}
   jobTemplate:
     spec:
       template:
         spec:
+          {{- if $cronjob.securityContext }}
           securityContext:
-            {{- toYaml .Values.securityContext | nindent 12 }}
-          {{- with .Values.nodeSelector }}
+            {{- toYaml $cronjob.securityContext | nindent 12 }}
+          {{- end}}
+          {{- if $cronjob.nodeSelector }}
           nodeSelector:
-            {{- toYaml . | nindent 16 }}
+            {{- toYaml $cronjob.nodeSelector | nindent 12 }}
+          {{- else if $.Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml $.Values.nodeSelector | nindent 12 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
+          - name: galaxy-cron-{{ $key }}
+            {{- if $cronjob.image }}
+            image: {{ $cronjob.image.repository }}:{{ $cronjob.image.tag }}
+            {{- else }}
+            image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
+            {{- end }}
+            imagePullPolicy: {{ $.Values.image.pullPolicy }}
+            {{- if or $cronjob.defaultEnv $cronjob.extraEnv }}
+            env:
+            {{- if $cronjob.defaultEnv }}
+            {{- include "galaxy.podEnvVars" $}}
+            {{- end }}
+            {{- if $cronjob.extraEnv }}
+            {{- range $env := $cronjob.extraEnv }}
+            - name: {{ $env.name }}
+              value: {{ tpl $env.value $ | quote }}
+            {{- end }}
+            {{- end }}
+            {{- end }}
             command:
-              - find
-              - {{ .Values.persistence.mountPath }}/tmp
-              - '!'
-              - -newermt
-              - -{{ (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) }} seconds
-              - -type
-              - f
-              - -exec
-              - rm
-              - '{}'
-              - ;
+            {{- range $cmd := $cronjob.command }}
+              - {{ tpl $cmd $ | quote }}
+            {{- end}}
+            {{- if $cronjob.args }}
+            args:
+              {{- range $arg := $cronjob.args }}
+              - {{ tpl $arg $ | quote }}
+              {{- end }}
+            {{- end }}
             volumeMounts:
             - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
+              mountPath: {{ $.Values.persistence.mountPath }}
+            {{- range $key, $entry := $cronjob.extraFileMappings }}
+            - name: {{ include "galaxy.getExtraFilesUniqueName" $key }}
+              mountPath: {{ $key }}
+              subPath: {{ include "galaxy.getFilenameFromPath" $key }}
+            {{- end }}
           volumes:
           - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
+            {{- if $.Values.persistence.enabled }}
             persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
+              claimName: {{ template "galaxy.pvcname" $ }}
             {{- else }}
             emptyDir: {}
             {{- end }}
+          {{- range $key, $entry := $cronjob.extraFileMappings }}
+          - name: {{ include "galaxy.getExtraFilesUniqueName" $key }}
+            {{- if $entry.useSecret }}
+            secret:
+              secretName: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $key) }}
+            {{- else }}
+            configMap:
+              name: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $key) }}
+            {{- end }}
+            {{- if $entry.mode }}
+              defaultMode: {{ $entry.mode }}
+            {{- end }}
+          {{- end }}
           restartPolicy: OnFailure
+{{- if $cronjob.extraFileMappings }}
+{{- range $name, $entry := $cronjob.extraFileMappings }}
+---
+apiVersion: v1
+metadata:
+  # Extract the filename portion only
+  name: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $name) }}
+  labels:
+    {{- include "galaxy.labels" $ | nindent 4 }}
+{{- if $entry.useSecret }}
+kind: Secret
+type: Opaque
+stringData:
+{{- else }}
+kind: ConfigMap
+data:
+{{- end }}
+  {{- include "galaxy.getFilenameFromPath" $name | nindent 2 }}: |
+  {{- if $entry.tpl }}
+    {{- tpl (tpl $entry.content $) $ | nindent 4 }}
+  {{- else }}
+    {{- $entry.content | nindent 4 }}
+  {{- end }}
+{{- end }}
+{{- end }}
+
+{{- end }}
diff --git a/galaxy/templates/deployment-celery-beat.yaml b/galaxy/templates/deployment-celery-beat.yaml
index e50a9622..0f46248d 100644
--- a/galaxy/templates/deployment-celery-beat.yaml
+++ b/galaxy/templates/deployment-celery-beat.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/deployment-celery.yaml b/galaxy/templates/deployment-celery.yaml
index c21660f4..100b4ac6 100644
--- a/galaxy/templates/deployment-celery.yaml
+++ b/galaxy/templates/deployment-celery.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/deployment-job.yaml b/galaxy/templates/deployment-job.yaml
index 28e12dc3..29988bd1 100644
--- a/galaxy/templates/deployment-job.yaml
+++ b/galaxy/templates/deployment-job.yaml
@@ -1,4 +1,5 @@
 {{- range $handler_num, $e := until (int $.Values.jobHandlers.replicaCount) }}
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
@@ -210,5 +211,4 @@ spec:
       tolerations:
         {{- toYaml . | nindent 8 }}
     {{- end }}
----
 {{- end }}
diff --git a/galaxy/templates/deployment-metrics.yaml b/galaxy/templates/deployment-metrics.yaml
index c3237716..87fa9dee 100644
--- a/galaxy/templates/deployment-metrics.yaml
+++ b/galaxy/templates/deployment-metrics.yaml
@@ -1,4 +1,5 @@
 {{- if .Values.metrics.enabled }}
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/deployment-nginx.yaml b/galaxy/templates/deployment-nginx.yaml
index 34020fcb..36d0bb6d 100644
--- a/galaxy/templates/deployment-nginx.yaml
+++ b/galaxy/templates/deployment-nginx.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/deployment-tusd.yaml b/galaxy/templates/deployment-tusd.yaml
index 45813ab9..0d7d2fb7 100644
--- a/galaxy/templates/deployment-tusd.yaml
+++ b/galaxy/templates/deployment-tusd.yaml
@@ -1,4 +1,5 @@
 {{ if .Values.tusd.enabled -}}
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/deployment-web.yaml b/galaxy/templates/deployment-web.yaml
index 0a1f8c49..783d1a52 100644
--- a/galaxy/templates/deployment-web.yaml
+++ b/galaxy/templates/deployment-web.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/deployment-workflow.yaml b/galaxy/templates/deployment-workflow.yaml
index ee094f58..b994fbc9 100644
--- a/galaxy/templates/deployment-workflow.yaml
+++ b/galaxy/templates/deployment-workflow.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: apps/v1
 kind: Deployment
 metadata:
diff --git a/galaxy/templates/hook-cvmfs-fix.yaml b/galaxy/templates/hook-cvmfs-fix.yaml
index 1caa21ba..7e88b036 100644
--- a/galaxy/templates/hook-cvmfs-fix.yaml
+++ b/galaxy/templates/hook-cvmfs-fix.yaml
@@ -1,5 +1,6 @@
 {{- if and .Values.refdata.enabled (eq .Values.refdata.type "cvmfs") }}
-  # Include the code you want to run when both conditions are met
+---
+# Include the code you want to run when both conditions are met
 apiVersion: batch/v1
 kind: Job
 metadata:
diff --git a/galaxy/templates/ingress-activity-canary.yaml b/galaxy/templates/ingress-activity-canary.yaml
index 09c467e1..4cee4b9e 100644
--- a/galaxy/templates/ingress-activity-canary.yaml
+++ b/galaxy/templates/ingress-activity-canary.yaml
@@ -6,6 +6,7 @@
 {{- $fullName := include "galaxy.fullname" . -}}
 {{- $ingressPath := .Values.ingress.path -}}
 {{- $servicePort := .Values.service.port -}}
+---
 apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
@@ -42,4 +43,4 @@ spec:
                   number: {{ $servicePort }}
     {{- end }}
 {{- end }}
----
+
diff --git a/galaxy/templates/ingress-tusd.yaml b/galaxy/templates/ingress-tusd.yaml
index ebb836a9..36180356 100644
--- a/galaxy/templates/ingress-tusd.yaml
+++ b/galaxy/templates/ingress-tusd.yaml
@@ -1,5 +1,6 @@
 {{- if and .Values.tusd.enabled .Values.tusd.ingress.enabled -}}
 {{- $fullName := include "galaxy.fullname" . -}}
+---
 apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
@@ -38,4 +39,4 @@ spec:
           {{- end }}
     {{- end }}
   {{- end }}
----
+
diff --git a/galaxy/templates/ingress.yaml b/galaxy/templates/ingress.yaml
index 9b2458e6..a77b9a2d 100644
--- a/galaxy/templates/ingress.yaml
+++ b/galaxy/templates/ingress.yaml
@@ -1,6 +1,7 @@
 {{- if .Values.ingress.enabled -}}
 {{- $fullName := include "galaxy.fullname" . -}}
 {{- $servicePort := .Values.service.port -}}
+---
 apiVersion: networking.k8s.io/v1
 kind: Ingress
 metadata:
@@ -39,4 +40,3 @@ spec:
           {{- end }}
     {{- end }}
   {{- end }}
----
diff --git a/galaxy/templates/jobs-init.yaml b/galaxy/templates/jobs-init.yaml
index d72244da..92079e07 100644
--- a/galaxy/templates/jobs-init.yaml
+++ b/galaxy/templates/jobs-init.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: batch/v1
 kind: Job
 metadata:
diff --git a/galaxy/templates/priorityclass-job.yaml b/galaxy/templates/priorityclass-job.yaml
index df518387..da4f9b59 100644
--- a/galaxy/templates/priorityclass-job.yaml
+++ b/galaxy/templates/priorityclass-job.yaml
@@ -1,4 +1,5 @@
 {{- if and .Values.jobs.priorityClass.enabled (not .Values.jobs.priorityClass.existingClass) }}
+---
 apiVersion: scheduling.k8s.io/v1
 kind: PriorityClass
 metadata:
diff --git a/galaxy/templates/pv-s3fs.yaml b/galaxy/templates/pv-s3fs.yaml
index 2948960c..4b0fb2fd 100644
--- a/galaxy/templates/pv-s3fs.yaml
+++ b/galaxy/templates/pv-s3fs.yaml
@@ -1,4 +1,5 @@
 {{- if and .Values.refdata.enabled (eq .Values.refdata.type "s3csi") }}
+---
 apiVersion: v1
 kind: PersistentVolume
 metadata:
diff --git a/galaxy/templates/pvc-galaxy.yaml b/galaxy/templates/pvc-galaxy.yaml
index c6426020..975f5c53 100644
--- a/galaxy/templates/pvc-galaxy.yaml
+++ b/galaxy/templates/pvc-galaxy.yaml
@@ -1,4 +1,5 @@
 {{ if and .Values.persistence.enabled (not .Values.persistence.existingClaim) -}}
+---
 apiVersion: v1
 kind: PersistentVolumeClaim
 metadata:
@@ -23,4 +24,3 @@ spec:
     requests:
       storage: {{ .Values.persistence.size | quote }}
 {{ end }}
----
diff --git a/galaxy/templates/pvc-refdata.yaml b/galaxy/templates/pvc-refdata.yaml
index a537eb03..a258f92b 100644
--- a/galaxy/templates/pvc-refdata.yaml
+++ b/galaxy/templates/pvc-refdata.yaml
@@ -1,4 +1,5 @@
 {{- if .Values.refdata.enabled }}
+---
 apiVersion: v1
 kind: PersistentVolumeClaim
 metadata:
@@ -18,5 +19,4 @@ spec:
 {{- if eq $.Values.refdata.type "cvmfs" }}
   storageClassName: {{ tpl .Values.cvmfs.storageClassName . }}
 {{- end }}
----
 {{- end }}
diff --git a/galaxy/templates/rabbitmqcluster.yaml b/galaxy/templates/rabbitmqcluster.yaml
index f215fc3b..1b100004 100644
--- a/galaxy/templates/rabbitmqcluster.yaml
+++ b/galaxy/templates/rabbitmqcluster.yaml
@@ -1,4 +1,5 @@
 {{- if and .Values.rabbitmq.enabled (not .Values.rabbitmq.existingCluster) }}
+---
 apiVersion: rabbitmq.com/v1beta1
 kind: RabbitmqCluster
 metadata:
diff --git a/galaxy/templates/rbac-job.yaml b/galaxy/templates/rbac-job.yaml
index f1180267..f80b5e1a 100644
--- a/galaxy/templates/rbac-job.yaml
+++ b/galaxy/templates/rbac-job.yaml
@@ -1,4 +1,5 @@
 {{ if .Values.rbac.enabled }}
+---
 kind: Role
 apiVersion: rbac.authorization.k8s.io/v1
 metadata:
diff --git a/galaxy/templates/secret-galaxy.yaml b/galaxy/templates/secret-galaxy.yaml
index bc0ffe52..6020642d 100644
--- a/galaxy/templates/secret-galaxy.yaml
+++ b/galaxy/templates/secret-galaxy.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 kind: Secret
 type: Opaque
diff --git a/galaxy/templates/service-galaxy.yaml b/galaxy/templates/service-galaxy.yaml
index 35fd5a1f..666dc20c 100644
--- a/galaxy/templates/service-galaxy.yaml
+++ b/galaxy/templates/service-galaxy.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 kind: Service
 metadata:
diff --git a/galaxy/templates/service-nginx.yaml b/galaxy/templates/service-nginx.yaml
index 1b1e9f04..c2cef838 100644
--- a/galaxy/templates/service-nginx.yaml
+++ b/galaxy/templates/service-nginx.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: v1
 kind: Service
 metadata:
diff --git a/galaxy/templates/service-tusd.yaml b/galaxy/templates/service-tusd.yaml
index 0f4a7454..572848eb 100644
--- a/galaxy/templates/service-tusd.yaml
+++ b/galaxy/templates/service-tusd.yaml
@@ -1,4 +1,5 @@
 {{ if .Values.tusd.enabled -}}
+---
 apiVersion: v1
 kind: Service
 metadata:
diff --git a/galaxy/templates/serviceaccount.yaml b/galaxy/templates/serviceaccount.yaml
index 8560763e..435da946 100644
--- a/galaxy/templates/serviceaccount.yaml
+++ b/galaxy/templates/serviceaccount.yaml
@@ -1,4 +1,5 @@
 {{- if .Values.serviceAccount.create -}}
+---
 apiVersion: v1
 kind: ServiceAccount
 metadata:
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 09d50603..c1d694a3 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -10,7 +10,7 @@ image:
   #- Repository containing the Galaxy image.
   repository: quay.io/galaxyproject/galaxy-anvil
   #- Galaxy Docker image tag (generally corresponds to the desired Galaxy version)
-  tag: "24.0"  # Value must be quoted
+  tag: "24.1.1"  # Galaxy versions prior to 24.1.1 contain a bug mapping the extra_files directory
   #-  Galaxy image [pull policy](https://kubernetes.io/docs/concepts/configuration/overview/#container-images)
   pullPolicy: IfNotPresent
 
@@ -267,10 +267,93 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
+#- CronJobs to perform periodic maintenance tasks
+cronJobs:
+  #- Runs the maintenance.sh script to purge items in the Galaxy database that
+  #- have been flagged as deleted.
+  maintenance:
+    enabled: true
+    schedule: "5 2 * * *"
+    extraSettings:
+      #- Purge items older than this.
+      days: '7'
+    securityContext:
+      runAsUser: 0
+    defaultEnv: true
+    command:
+      - "/galaxy/server/scripts/maintenance.sh"
+    args:
+      - "--no-dry-run"
+      - "--days"
+      - "{{ tpl .Values.cronJobs.maintenance.extraSettings.days $ }}"
+  #- Remove files from the tmp directory that are older than the allowable wall time for a job
+  tmpdir:
+    enabled: true
+    schedule: "15 2 * * *"
+    extraSettings:
+      lastModified: '{{ index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800 }}'
+    securityContext:
+      runAsUser: 0
+    command:
+      - /usr/bin/find
+    args:
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "!"
+      - "-newermt"
+      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.lastModified $ }} seconds ago"
+      - "-type"
+      - "f"
+      - "-exec"
+      - "rm"
+      - "{}"
+      - ";"
+#  #- An example cron job that showcases all available features.
+#  example:
+#    #- Disable the job by scheduling it for a date that never occurs, I.E. Feb 30th
+#    #- The job can still be triggered manually.
+#    schedule: "0 0 30 2 *"
+#    #- Include the set of default environment variables. See galaxy.podEnvVars
+#    #- in the Helm chart's _helpers.tpl for the variables that will be defined.
+#    defaultEnv: true
+#    #- Define extra environment variables that will be available to the job
+#    extraEnv:
+#      - name: LOGFILE
+#        value: /galaxy/server/database/example.log
+#    #- Run the job as root (uid 0)
+#    securityContext:
+#      runAsUser: 0
+#    #- Specify an alternate Docker image for the CronJob container
+#    image:
+#      repository: ksuderman/galaxy-maintenance
+#      tag: "0.7"
+#    #- The command to be run
+#    command:
+#      - /usr/local/bin/example.sh
+#    #- Command line arguments to be passed to the command, one per line.
+#    args:
+#      - "--option"
+#      - "value"
+#    #- Define extra files that will be mounted into the image. In this case we
+#    #- mount a simple Bash script that will write the current environment
+#    #- variables to persistent storage.
+#    extraFileMappings:
+#      #- Path were the file will be mounted
+#      /usr/local/bin/example.sh:
+#        #- Default permission on the file.  In this case 'rwxr-xr-x'
+#        mode: "0755"
+#        #- Run the contents through the Helm `tpl` command
+#        tpl: true
+#        #- The contents of the file to be mounted.  Can contain Helm template values
+#        #- if `tpl` is set to true.
+#        content: |-
+#          #!/usr/bin/bash
+#          echo {{ .Release.Name }} >> $LOGFILE
+#          echo "$@" >> $LOGFILE
+#          env >> $LOGFILE
+
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true
-  #-
   ingressClassName: nginx
   canary:
     enabled: true
@@ -391,13 +474,21 @@ configs:
       k8s:
         load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
         k8s_use_service_account: true
-        k8s_persistent_volume_claims: |-
+        k8s_data_volume_claim: |-
+          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
+        k8s_working_volume_claim: |-
           {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
+        k8s_persistent_volume_claims: |-
+          {{ template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config:r,
+          {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp:rw,
+          {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data:rw,
+          {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools:r,
+          {{- template "galaxy.pvcname" . -}}/shed_tools:{{ .Values.persistence.mountPath -}}/shed_tools:r
           {{- if .Values.refdata.enabled -}}
-          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org
+          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:r
           {{- end -}}
           {{- if .Values.setupJob.downloadToolConfs.enabled -}}
-          ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}
+          ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}:r
           {{- end -}}
           {{- if .Values.extraVolumes -}}
           {{- template "galaxy.extra_pvc_mounts" . -}}
@@ -451,7 +542,8 @@ configs:
       interactivetools_base_path: "{{$host := index .Values.ingress.hosts 0}}{{$path := index $host.paths 0}}{{$path.path}}"
       id_secret:
       mulled_resolution_cache_lock_dir: "/galaxy/server/local/mulled_cache_lock"
-      database_connection: postgresql://unused:because@overridden_by_envvar
+      database_connection: |-
+        {{ include "galaxy-postgresql.connection-string" .}}
       integrated_tool_panel_config: "/galaxy/server/config/mutable/integrated_tool_panel.xml"
       sanitize_allowlist_file: "/galaxy/server/config/mutable/sanitize_allowlist.txt"
       tool_config_file: "/galaxy/server/config/tool_conf.xml{{if .Values.setupJob.downloadToolConfs.enabled}},{{ .Values.setupJob.downloadToolConfs.volume.mountPath }}/config/shed_tool_conf.xml{{end}}"
@@ -506,22 +598,35 @@ configs:
     toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0
     toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0
     toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
-    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
+    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
     toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
+    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
+    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72
+    toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.44+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy2
+    toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1
-    toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1
+    toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6
     toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/5.0.5.0
+    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
     toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
+    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
+    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
+    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0
     toolshed.g2.bx.psu.edu/repos/iuc/prestor_abseq3/prestor_abseq3/0.6.2+galaxy0
     toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3
     toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.1.0+galaxy0
+    toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1
+    toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2
     toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
+    toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1
+    toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2
+    toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1
   build_sites.yml:
     - type: ucsc
       file: "{{if .Values.refdata.enabled}}/cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt{{else}}/galaxy/server/tool-data/shared/ucsc/ucsc_build_sites.txt.sample{{end}}"