From 4e27f15ed2ec1c526cccc66c6010e0804688e6c0 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <almahmoud@jhu.edu>
Date: Fri, 13 Aug 2021 19:16:32 -0400
Subject: [PATCH 01/68] Changes for not mounting entire NFS to each job

friends with https://github.com/galaxyproject/galaxy/pull/12345
---
 galaxy/values.yaml | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 8cfd4e97..02eb3105 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -273,11 +273,20 @@ 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_persistent_volume_claims: |-
+          {{ template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache,
+          {{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config,
+          {{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps,
+          {{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache,
+          {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp,
+          {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data,
+          {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools,
+          {{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index
           {{- if .Values.cvmfs.enabled -}}
           {{- range $key, $entry := .Values.cvmfs.galaxyPersistentVolumeClaims -}}
-          ,{{- template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}}
+          ,{{ template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}}
           {{- end -}}
           {{- end -}}
           {{- if .Values.initJob.downloadToolConfs.enabled -}}

From bb53d371a72ba298a64f16d17328b26584608388 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <almahmoud@jhu.edu>
Date: Mon, 30 Aug 2021 15:47:42 -0400
Subject: [PATCH 02/68] Separate data and working dir pvcs

---
 galaxy/values.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 02eb3105..fb569a81 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -275,6 +275,8 @@ configs:
         k8s_use_service_account: true
         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" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache,
           {{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config,

From 380430dd51ada4def02cafcdc7733d5bccc5adce Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Mon, 20 Dec 2021 19:29:32 +0530
Subject: [PATCH 03/68] Removed unnecessary mounts and made inputs read only

---
 galaxy/values.yaml | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index fb569a81..fe0ef196 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -274,18 +274,14 @@ configs:
         load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
         k8s_use_service_account: true
         k8s_data_volume_claim: |-
-          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
+          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}:r
         k8s_working_volume_claim: |-
           {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
         k8s_persistent_volume_claims: |-
-          {{ template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache,
-          {{- template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config,
-          {{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps,
-          {{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache,
-          {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp,
-          {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data,
-          {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools,
-          {{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index
+          {{ 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:r,
+          {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools:r
           {{- if .Values.cvmfs.enabled -}}
           {{- range $key, $entry := .Values.cvmfs.galaxyPersistentVolumeClaims -}}
           ,{{ template "galaxy.fullname" $ -}}-cvmfs-gxy-{{ $key }}-pvc:{{ $entry.mountPath -}}

From 32dc5a1e11e94e041f61e8897e1ffdb732a8767c Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Mon, 10 Apr 2023 15:36:15 -0400
Subject: [PATCH 04/68] Add a section for Expression Tools and the
 param_value_from_file tool

---
 galaxy/files/configs/tool_conf.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/galaxy/files/configs/tool_conf.xml b/galaxy/files/configs/tool_conf.xml
index 6870427f..840aa27e 100644
--- a/galaxy/files/configs/tool_conf.xml
+++ b/galaxy/files/configs/tool_conf.xml
@@ -38,6 +38,9 @@
     <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"/>
+  </section>
   <label id="general_text_label" text="General Text Tools" />
   <section id="text_manipulation" name="Text Manipulation">
     <tool file="filters/fixedValueColumn.xml" />

From 9de3819ee167f0893fe0a0957201fb4a4b60010c Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 19 Apr 2023 19:21:51 -0400
Subject: [PATCH 05/68] Add the pick_value tool

---
 galaxy/files/configs/tool_conf.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/galaxy/files/configs/tool_conf.xml b/galaxy/files/configs/tool_conf.xml
index 840aa27e..381ab817 100644
--- a/galaxy/files/configs/tool_conf.xml
+++ b/galaxy/files/configs/tool_conf.xml
@@ -40,6 +40,7 @@
   </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">

From 4138130ba69508a19c1f6431970251d2e4c703ca Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 9 Feb 2024 16:19:30 -0500
Subject: [PATCH 06/68] Remove spaces that makes helm lint unhappy

---
 galaxy/templates/hook-cvmfs-fix.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/templates/hook-cvmfs-fix.yaml b/galaxy/templates/hook-cvmfs-fix.yaml
index 1caa21ba..a91a76bf 100644
--- a/galaxy/templates/hook-cvmfs-fix.yaml
+++ b/galaxy/templates/hook-cvmfs-fix.yaml
@@ -1,5 +1,5 @@
 {{- 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:

From e0b960dadf8dc2495d6f6067f2a886dd21b1ef0b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 9 Feb 2024 16:20:10 -0500
Subject: [PATCH 07/68] First pass at defining cron jobs in the values.yaml
 file.

---
 galaxy/templates/cronjob-maintenance.yaml | 46 ++++++++---------
 galaxy/values.yaml                        | 63 ++++++++++++++++++++++-
 2 files changed, 85 insertions(+), 24 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 17b0219a..a9344494 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,47 +1,47 @@
+{{ if .Values.cronJobs -}}
+{{ range $key, $cronjob := .Values.cronJobs }}
+---
 apiVersion: batch/v1
 kind: CronJob
 metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance
+  name: {{ include "galaxy.fullname" $ }}-maintenance-{{ $key }}
   labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
+    {{- include "galaxy.labels" $ | nindent 4 }}
 spec:
-  schedule: "0 2 * * *"
+  schedule: {{ $cronjob.schedule | quote }}
   jobTemplate:
     spec:
       template:
         spec:
           securityContext:
-            {{- toYaml .Values.securityContext | nindent 12 }}
-          {{- with .Values.nodeSelector }}
+            {{- toYaml $cronjob.securityContext | nindent 12 }}
+          {{- with $.nodeSelector }}
           nodeSelector:
             {{- toYaml . | nindent 16 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
+          - name: galaxy-maintenance-{{ $key }}
+            image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
+            imagePullPolicy: {{ $.Values.image.pullPolicy }}
             # delete all tmp files older than walltime limit
-            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
-              - '{}'
-              - ;
+            command: {{ $cronjob.command }}
+            {{- if $cronjob.args }}
+            args:
+              {{- range $arg := $cronjob.args }}
+              - {{ tpl $arg $ }}
+              {{- end }}
+            {{- end }}
             volumeMounts:
             - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
+              mountPath: {{ $.Values.persistence.mountPath }}
           volumes:
           - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
+            {{- if $.Values.persistence.enabled }}
             persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
+              claimName: {{ template "galaxy.pvcname" $ }}
             {{- else }}
             emptyDir: {}
             {{- end }}
           restartPolicy: OnFailure
+{{- end }}
+{{- end }}
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 9c85c0c0..ad8e3e25 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -267,6 +267,66 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
+cronJobs:
+  clean-tmp:
+    schedule: "0 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /bin/bash
+    args:
+      - "-c"
+      - "find"
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "!"
+      - "-newermt"
+      - "-{{ (index .Values \"configs\" \"job_conf.yml\" \"runners\" \"k8s\" \"k8s_walltime_limit\" | default 604800) }} seconds"
+      - "-type"
+      - "f"
+      - "-exec"
+      - "rm"
+      - "{}"
+      - ";"
+  clean-jobs:
+    schedule: "10 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /usr/bin/tmpwatch
+    args:
+      - "-v"
+      - "--all"
+      - "--mtime"
+      - "--dirmtime"
+      - "7d"
+      - "{{ .Values.persistence.mountPath }}/jobs_directory"
+  cleanup-datasets:
+    schedule: "20 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /galaxy/server/.venv/bin/python
+    args:
+    - "/galaxy/server/scripts/cleanup_datasets/pgcleanup.py"
+    - "-c"
+    - "/galaxy/server/config/galaxy.yml"
+    - "-o"
+    - "7"
+    - "-l"
+    - "{{ .Values.persistence.mountPath }}/tmp"
+    - "-w"
+    - "128MB"
+    - "delete_userless_histories"
+    - "delete_exported_histories"
+  cleanup-tusd-store:
+    schedule: "30 2 * * *"
+    securityContext:
+      runAsUser: 0
+    command: /usr/bin/tmpwatch
+    args:
+    - "-v"
+    - "--all"
+    - "--mtime"
+    - "--dirmtime"
+    - "7d"
+    - "{{ .Values.persistence.mountPath }}/tmp/tus_upload_store"
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true
@@ -301,7 +361,8 @@ resources:
     memory: 7G
     ephemeral-storage: 10Gi
 
-nodeSelector: {}
+#nodeSelector: {}
+nodeSelector: "cloud:google:com/gke-nodepool: default-pool"
 
 tolerations: []
 

From 9c84d17cfc3ce76d0df53d4590646e904e1ebdad Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 13 Feb 2024 08:07:27 -0500
Subject: [PATCH 08/68] Fix command formatting and quoting

---
 galaxy/templates/cronjob-maintenance.yaml |  7 +++-
 galaxy/values.yaml                        | 49 +++++++++++++----------
 2 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index a9344494..2ae3bde6 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -24,11 +24,14 @@ spec:
             image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
             imagePullPolicy: {{ $.Values.image.pullPolicy }}
             # delete all tmp files older than walltime limit
-            command: {{ $cronjob.command }}
+            command:
+            {{- range $cmd := $cronjob.command }}
+              - {{ tpl $cmd $ | quote }}
+            {{- end}}
             {{- if $cronjob.args }}
             args:
               {{- range $arg := $cronjob.args }}
-              - {{ tpl $arg $ }}
+              - {{ tpl $arg $ | quote }}
               {{- end }}
             {{- end }}
             volumeMounts:
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index ad8e3e25..7dba17cd 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -272,14 +272,16 @@ cronJobs:
     schedule: "0 2 * * *"
     securityContext:
       runAsUser: 0
-    command: /bin/bash
+    command:
+      - "/bin/bash"
     args:
       - "-c"
       - "find"
       - "{{ .Values.persistence.mountPath }}/tmp"
       - "!"
       - "-newermt"
-      - "-{{ (index .Values \"configs\" \"job_conf.yml\" \"runners\" \"k8s\" \"k8s_walltime_limit\" | default 604800) }} seconds"
+      - "-{{ (index .Values \"configs\" \"job_conf.yml\" \"runners\" \"k8s\" \"k8s_walltime_limit\" | default 604800) }}"
+      - "seconds"
       - "-type"
       - "f"
       - "-exec"
@@ -290,7 +292,8 @@ cronJobs:
     schedule: "10 2 * * *"
     securityContext:
       runAsUser: 0
-    command: /usr/bin/tmpwatch
+    command:
+      - "/usr/bin/tmpwatch"
     args:
       - "-v"
       - "--all"
@@ -302,31 +305,33 @@ cronJobs:
     schedule: "20 2 * * *"
     securityContext:
       runAsUser: 0
-    command: /galaxy/server/.venv/bin/python
+    command:
+      - "/galaxy/server/.venv/bin/python"
     args:
-    - "/galaxy/server/scripts/cleanup_datasets/pgcleanup.py"
-    - "-c"
-    - "/galaxy/server/config/galaxy.yml"
-    - "-o"
-    - "7"
-    - "-l"
-    - "{{ .Values.persistence.mountPath }}/tmp"
-    - "-w"
-    - "128MB"
-    - "delete_userless_histories"
-    - "delete_exported_histories"
+      - "/galaxy/server/scripts/cleanup_datasets/pgcleanup.py"
+      - "-c"
+      - "/galaxy/server/config/galaxy.yml"
+      - "-o"
+      - "7"
+      - "-l"
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "-w"
+      - "128MB"
+      - "delete_userless_histories"
+      - "delete_exported_histories"
   cleanup-tusd-store:
     schedule: "30 2 * * *"
     securityContext:
       runAsUser: 0
-    command: /usr/bin/tmpwatch
+    command:
+      - "/usr/bin/tmpwatch"
     args:
-    - "-v"
-    - "--all"
-    - "--mtime"
-    - "--dirmtime"
-    - "7d"
-    - "{{ .Values.persistence.mountPath }}/tmp/tus_upload_store"
+      - "-v"
+      - "--all"
+      - "--mtime"
+      - "--dirmtime"
+      - "7d"
+      - "{{ .Values.persistence.mountPath }}/tmp/tus_upload_store"
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true

From d2941d7f78a1bbed894ffd0ae6844393932ea00b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 13 Feb 2024 09:24:57 -0500
Subject: [PATCH 09/68] Remove nodeSelector

---
 galaxy/values.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 7dba17cd..c977e821 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -366,8 +366,7 @@ resources:
     memory: 7G
     ephemeral-storage: 10Gi
 
-#nodeSelector: {}
-nodeSelector: "cloud:google:com/gke-nodepool: default-pool"
+nodeSelector: {}
 
 tolerations: []
 

From 95474e2b3e7327155c720adbf1ae8fb9e6b1ef0f Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 16 Feb 2024 13:21:22 -0500
Subject: [PATCH 10/68] Tmp cleanup and maintenance scripts are treated as
 special cases.

---
 galaxy/templates/cronjob-maintenance.yaml | 99 +++++++++++++++++++++++
 galaxy/values.yaml                        | 78 +++++-------------
 2 files changed, 118 insertions(+), 59 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 2ae3bde6..2d1aa39b 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,3 +1,100 @@
+{{- if .Values.maintenance.tmp.enabled }}
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: {{ include "galaxy.fullname" . }}-maintenance-clean-tmp
+  labels:
+    {{- include "galaxy.labels" . | nindent 4 }}
+spec:
+  schedule: {{ .Values.maintenance.tmp.schedule | quote }}
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          securityContext:
+            runAsUser: 0
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          {{- with .Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 16 }}
+          {{- end }}
+          containers:
+          - name: galaxy-maintenance-clean-tmp
+            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+            imagePullPolicy: {{ .Values.image.pullPolicy }}
+            # delete all tmp files older than walltime limit
+            command:
+              - find
+              - {{ .Values.persistence.mountPath }}/tmp
+              - '!'
+              - -newermt
+              - "{{ .Values.maintenance.tmp.seconds }} seconds"
+              - -type
+              - f
+              - -exec
+              - rm
+              - '{}'
+              - ;
+            volumeMounts:
+            - name: galaxy-data
+              mountPath: {{ .Values.persistence.mountPath }}
+          volumes:
+          - name: galaxy-data
+            {{- if .Values.persistence.enabled }}
+            persistentVolumeClaim:
+              claimName: {{ template "galaxy.pvcname" . }}
+            {{- else }}
+            emptyDir: {}
+            {{- end }}
+          restartPolicy: OnFailure
+{{- end }}
+{{- if .Values.maintenance.script.enabled }}
+---
+apiVersion: batch/v1
+kind: CronJob
+metadata:
+  name: {{ include "galaxy.fullname" . }}-maintenance-script
+  labels:
+    {{- include "galaxy.labels" . | nindent 4 }}
+spec:
+  schedule: {{ .Values.maintenance.script.schedule | quote }}
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          securityContext:
+            runAsUser: 0
+          {{- with .Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml . | nindent 16 }}
+          {{- end }}
+          containers:
+          - name: galaxy-maintenance
+            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
+            imagePullPolicy: {{ .Values.image.pullPolicy }}
+            # delete all tmp files older than walltime limit
+            command:
+              - "/bin/bash"
+              - "-c"
+            args:
+              - "/galaxy/server/scripts/maintenance.sh"
+              - "--no-dry-run"
+              - "--days"
+              - {{ .Values.maintenance.script.days | quote }}
+            volumeMounts:
+            - name: galaxy-data
+              mountPath: {{ .Values.persistence.mountPath }}
+          volumes:
+          - name: galaxy-data
+            {{- if .Values.persistence.enabled }}
+            persistentVolumeClaim:
+              claimName: {{ template "galaxy.pvcname" . }}
+            {{- else }}
+            emptyDir: {}
+            {{- end }}
+          restartPolicy: OnFailure
+{{- end }}
 {{ if .Values.cronJobs -}}
 {{ range $key, $cronjob := .Values.cronJobs }}
 ---
@@ -13,8 +110,10 @@ spec:
     spec:
       template:
         spec:
+          {{- if $cronjob.securityContext }}
           securityContext:
             {{- toYaml $cronjob.securityContext | nindent 12 }}
+          {{- end}}
           {{- with $.nodeSelector }}
           nodeSelector:
             {{- toYaml . | nindent 16 }}
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index c977e821..fd821f04 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -267,71 +267,31 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
+#- User defined CronJobs
 cronJobs:
-  clean-tmp:
-    schedule: "0 2 * * *"
+  chown:
+    schedule: "0 * * * *"
     securityContext:
       runAsUser: 0
     command:
-      - "/bin/bash"
+      - /usr/bin/chown
     args:
-      - "-c"
-      - "find"
-      - "{{ .Values.persistence.mountPath }}/tmp"
-      - "!"
-      - "-newermt"
-      - "-{{ (index .Values \"configs\" \"job_conf.yml\" \"runners\" \"k8s\" \"k8s_walltime_limit\" | default 604800) }}"
-      - "seconds"
-      - "-type"
-      - "f"
-      - "-exec"
-      - "rm"
-      - "{}"
-      - ";"
-  clean-jobs:
+      - "-R"
+      - "galaxy"
+      - "/galaxy/server/database"
+#- Maintenance tasks that should be run periodically to prevent storage from being exhausted
+maintenance:
+  #- Remove files in the tmp directory.
+  tmp:
+    enabled: true
+    schedule: "5 2 * * *"
+    seconds: "604800" # Default wall time for jobs
+  #- The maintenance script removes histories, datasets, and other Galaxy objects older than 7 days.
+  script:
+    enabled: true
     schedule: "10 2 * * *"
-    securityContext:
-      runAsUser: 0
-    command:
-      - "/usr/bin/tmpwatch"
-    args:
-      - "-v"
-      - "--all"
-      - "--mtime"
-      - "--dirmtime"
-      - "7d"
-      - "{{ .Values.persistence.mountPath }}/jobs_directory"
-  cleanup-datasets:
-    schedule: "20 2 * * *"
-    securityContext:
-      runAsUser: 0
-    command:
-      - "/galaxy/server/.venv/bin/python"
-    args:
-      - "/galaxy/server/scripts/cleanup_datasets/pgcleanup.py"
-      - "-c"
-      - "/galaxy/server/config/galaxy.yml"
-      - "-o"
-      - "7"
-      - "-l"
-      - "{{ .Values.persistence.mountPath }}/tmp"
-      - "-w"
-      - "128MB"
-      - "delete_userless_histories"
-      - "delete_exported_histories"
-  cleanup-tusd-store:
-    schedule: "30 2 * * *"
-    securityContext:
-      runAsUser: 0
-    command:
-      - "/usr/bin/tmpwatch"
-    args:
-      - "-v"
-      - "--all"
-      - "--mtime"
-      - "--dirmtime"
-      - "7d"
-      - "{{ .Values.persistence.mountPath }}/tmp/tus_upload_store"
+    days: "7"
+
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true

From 93930d7d48c82b7baf62d237fb615e19950d1e71 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 16 Feb 2024 13:29:25 -0500
Subject: [PATCH 11/68] Update the name of the container used to run the
 maintenance script.

---
 galaxy/templates/cronjob-maintenance.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 2d1aa39b..9df57386 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -70,7 +70,7 @@ spec:
             {{- toYaml . | nindent 16 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance
+          - name: galaxy-maintenance-script
             image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
             imagePullPolicy: {{ .Values.image.pullPolicy }}
             # delete all tmp files older than walltime limit

From 287cf133f440a03b37cc3549e91462c745cf7844 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Mon, 19 Feb 2024 12:12:38 -0500
Subject: [PATCH 12/68] Define all cron jobs in the values.yaml file again, but
 allows time durations to be parameterized.

---
 galaxy/templates/cronjob-maintenance.yaml | 102 +---------------------
 galaxy/values.yaml                        |  46 +++++++---
 2 files changed, 35 insertions(+), 113 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 9df57386..3f626e35 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,101 +1,3 @@
-{{- if .Values.maintenance.tmp.enabled }}
----
-apiVersion: batch/v1
-kind: CronJob
-metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance-clean-tmp
-  labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
-spec:
-  schedule: {{ .Values.maintenance.tmp.schedule | quote }}
-  jobTemplate:
-    spec:
-      template:
-        spec:
-          securityContext:
-            runAsUser: 0
-            {{- toYaml .Values.securityContext | nindent 12 }}
-          {{- with .Values.nodeSelector }}
-          nodeSelector:
-            {{- toYaml . | nindent 16 }}
-          {{- end }}
-          containers:
-          - name: galaxy-maintenance-clean-tmp
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
-            command:
-              - find
-              - {{ .Values.persistence.mountPath }}/tmp
-              - '!'
-              - -newermt
-              - "{{ .Values.maintenance.tmp.seconds }} seconds"
-              - -type
-              - f
-              - -exec
-              - rm
-              - '{}'
-              - ;
-            volumeMounts:
-            - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
-          volumes:
-          - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
-            persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
-            {{- else }}
-            emptyDir: {}
-            {{- end }}
-          restartPolicy: OnFailure
-{{- end }}
-{{- if .Values.maintenance.script.enabled }}
----
-apiVersion: batch/v1
-kind: CronJob
-metadata:
-  name: {{ include "galaxy.fullname" . }}-maintenance-script
-  labels:
-    {{- include "galaxy.labels" . | nindent 4 }}
-spec:
-  schedule: {{ .Values.maintenance.script.schedule | quote }}
-  jobTemplate:
-    spec:
-      template:
-        spec:
-          securityContext:
-            runAsUser: 0
-          {{- with .Values.nodeSelector }}
-          nodeSelector:
-            {{- toYaml . | nindent 16 }}
-          {{- end }}
-          containers:
-          - name: galaxy-maintenance-script
-            image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-            imagePullPolicy: {{ .Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
-            command:
-              - "/bin/bash"
-              - "-c"
-            args:
-              - "/galaxy/server/scripts/maintenance.sh"
-              - "--no-dry-run"
-              - "--days"
-              - {{ .Values.maintenance.script.days | quote }}
-            volumeMounts:
-            - name: galaxy-data
-              mountPath: {{ .Values.persistence.mountPath }}
-          volumes:
-          - name: galaxy-data
-            {{- if .Values.persistence.enabled }}
-            persistentVolumeClaim:
-              claimName: {{ template "galaxy.pvcname" . }}
-            {{- else }}
-            emptyDir: {}
-            {{- end }}
-          restartPolicy: OnFailure
-{{- end }}
-{{ if .Values.cronJobs -}}
 {{ range $key, $cronjob := .Values.cronJobs }}
 ---
 apiVersion: batch/v1
@@ -116,13 +18,12 @@ spec:
           {{- end}}
           {{- with $.nodeSelector }}
           nodeSelector:
-            {{- toYaml . | nindent 16 }}
+            {{- toYaml . | nindent 12 }}
           {{- end }}
           containers:
           - name: galaxy-maintenance-{{ $key }}
             image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
             imagePullPolicy: {{ $.Values.image.pullPolicy }}
-            # delete all tmp files older than walltime limit
             command:
             {{- range $cmd := $cronjob.command }}
               - {{ tpl $cmd $ | quote }}
@@ -146,4 +47,3 @@ spec:
             {{- end }}
           restartPolicy: OnFailure
 {{- end }}
-{{- end }}
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index fd821f04..454215eb 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -279,19 +279,41 @@ cronJobs:
       - "-R"
       - "galaxy"
       - "/galaxy/server/database"
-#- Maintenance tasks that should be run periodically to prevent storage from being exhausted
-maintenance:
-  #- Remove files in the tmp directory.
-  tmp:
-    enabled: true
+  maintenance:
     schedule: "5 2 * * *"
-    seconds: "604800" # Default wall time for jobs
-  #- The maintenance script removes histories, datasets, and other Galaxy objects older than 7 days.
-  script:
-    enabled: true
-    schedule: "10 2 * * *"
-    days: "7"
-
+    extraSettings:
+      days: 7
+    securityContext:
+      runAsUser: 0
+    command:
+      - "/bin/bash"
+      - "-c"
+    args:
+      - "/galaxy/server/scripts/maintenance.sh"
+      - "--no-dry-run"
+      - "--days"
+      - "{{ .Values.cronJobs.maintenance.extraSettings.days }}"
+  #- Remove files from the tmp directory that are older than the allowable wall time for a job
+  tmp:
+    schedule: "15 2 * * *"
+    extraSettings:
+      seconds: 604800
+    securityContext:
+      runAsUser: 0
+    command:
+      - /usr/bin/find
+    args:
+      - "{{ .Values.persistence.mountPath }}/tmp"
+      - "!"
+      - "-newermt"
+      - "{{ .Values.cronJobs.tmp.extraSettings.seconds }}"
+      - "seconds"
+      - "-type"
+      - "f"
+      - "-exec"
+      - "rm"
+      - "{}"
+      - ";"
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true

From 8225be5590c53c6657d50f4562f4fc2d81bf71ba Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Wed, 21 Feb 2024 00:45:24 +0530
Subject: [PATCH 13/68] Use walltime limit for cleanup and other minor tweaks

---
 galaxy/templates/cronjob-maintenance.yaml |  4 ++--
 galaxy/values.yaml                        | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 3f626e35..3932f35d 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -3,7 +3,7 @@
 apiVersion: batch/v1
 kind: CronJob
 metadata:
-  name: {{ include "galaxy.fullname" $ }}-maintenance-{{ $key }}
+  name: {{ include "galaxy.fullname" $ }}-cron-{{ $key }}
   labels:
     {{- include "galaxy.labels" $ | nindent 4 }}
 spec:
@@ -21,7 +21,7 @@ spec:
             {{- toYaml . | nindent 12 }}
           {{- end }}
           containers:
-          - name: galaxy-maintenance-{{ $key }}
+          - name: galaxy-cron-{{ $key }}
             image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
             imagePullPolicy: {{ $.Values.image.pullPolicy }}
             command:
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 454215eb..a049f74d 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -282,7 +282,7 @@ cronJobs:
   maintenance:
     schedule: "5 2 * * *"
     extraSettings:
-      days: 7
+      days: '7'
     securityContext:
       runAsUser: 0
     command:
@@ -292,12 +292,12 @@ cronJobs:
       - "/galaxy/server/scripts/maintenance.sh"
       - "--no-dry-run"
       - "--days"
-      - "{{ .Values.cronJobs.maintenance.extraSettings.days }}"
+      - "{{ tpl .Values.cronJobs.maintenance.extraSettings.days $ }}"
   #- Remove files from the tmp directory that are older than the allowable wall time for a job
-  tmp:
+  tmpdir:
     schedule: "15 2 * * *"
     extraSettings:
-      seconds: 604800
+      days: '{{ div (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) 7 }}'
     securityContext:
       runAsUser: 0
     command:
@@ -306,7 +306,7 @@ cronJobs:
       - "{{ .Values.persistence.mountPath }}/tmp"
       - "!"
       - "-newermt"
-      - "{{ .Values.cronJobs.tmp.extraSettings.seconds }}"
+      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.days $ }}"
       - "seconds"
       - "-type"
       - "f"

From 8cc5d943e2239348dcfa1b9493e24610f7fd6b28 Mon Sep 17 00:00:00 2001
From: nuwang <2070605+nuwang@users.noreply.github.com>
Date: Wed, 21 Feb 2024 02:01:21 +0530
Subject: [PATCH 14/68] Change find units from seconds to days

---
 galaxy/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index a049f74d..b54813f1 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -307,7 +307,7 @@ cronJobs:
       - "!"
       - "-newermt"
       - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.days $ }}"
-      - "seconds"
+      - "days"
       - "-type"
       - "f"
       - "-exec"

From 64320c88cbaecaff12d06d14df0301f8e3b85a0d Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 21 Feb 2024 12:09:28 -0500
Subject: [PATCH 15/68] Parameterize the nodeSelector

---
 galaxy/templates/cronjob-maintenance.yaml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 3932f35d..6fa86432 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -16,9 +16,12 @@ spec:
           securityContext:
             {{- toYaml $cronjob.securityContext | nindent 12 }}
           {{- end}}
-          {{- with $.nodeSelector }}
+          {{- if $cronjob.nodeSelector }}
           nodeSelector:
-            {{- toYaml . | nindent 12 }}
+            {{- toYaml $cronjob.nodeSelector | nindent 12 }}
+          {{- else if $.Values.nodeSelector }}
+          nodeSelector:
+            {{- toYaml $.Values.nodeSelector | nindent 12 }}
           {{- end }}
           containers:
           - name: galaxy-cron-{{ $key }}

From 2bbaa3a875eec54d898f7d6d9b25ea688fc63e16 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 21 Feb 2024 12:34:40 -0500
Subject: [PATCH 16/68] Remove the chown cron job

---
 galaxy/values.yaml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index b54813f1..8f26de53 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -269,16 +269,6 @@ extraEnv: []
 
 #- User defined CronJobs
 cronJobs:
-  chown:
-    schedule: "0 * * * *"
-    securityContext:
-      runAsUser: 0
-    command:
-      - /usr/bin/chown
-    args:
-      - "-R"
-      - "galaxy"
-      - "/galaxy/server/database"
   maintenance:
     schedule: "5 2 * * *"
     extraSettings:

From df1fb39f8534f6a07f1878d9d2510e9a445088e8 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 21 Feb 2024 16:39:01 -0500
Subject: [PATCH 17/68] Reverting my revert

---
 galaxy/values.yaml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 8f26de53..a3861876 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -287,7 +287,7 @@ cronJobs:
   tmpdir:
     schedule: "15 2 * * *"
     extraSettings:
-      days: '{{ div (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) 7 }}'
+      last_modified: '{{ index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800 }}'
     securityContext:
       runAsUser: 0
     command:
@@ -296,8 +296,7 @@ cronJobs:
       - "{{ .Values.persistence.mountPath }}/tmp"
       - "!"
       - "-newermt"
-      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.days $ }}"
-      - "days"
+      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.last_modified $ }} seconds ago"
       - "-type"
       - "f"
       - "-exec"

From 247cbf5fb4992d13d7ee891415df17d688397663 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 28 Feb 2024 12:58:54 -0600
Subject: [PATCH 18/68] Add extraFileMappings for cron jobs

---
 galaxy/templates/cronjob-maintenance.yaml | 15 +++++++++++++++
 galaxy/values.yaml                        | 13 ++++++++++++-
 2 files changed, 27 insertions(+), 1 deletion(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 6fa86432..954304a5 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -40,6 +40,11 @@ spec:
             volumeMounts:
             - name: galaxy-data
               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 }}
@@ -48,5 +53,15 @@ spec:
             {{- 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 }}
+        {{- end }}
           restartPolicy: OnFailure
 {{- end }}
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index a3861876..1fc25660 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -267,8 +267,9 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
-#- User defined CronJobs
+#- CronJobs to perform periodic maintenacne tasks
 cronJobs:
+  #- Runs the maintenance.sh script to clean up the Galaxy database.
   maintenance:
     schedule: "5 2 * * *"
     extraSettings:
@@ -283,6 +284,16 @@ cronJobs:
       - "--no-dry-run"
       - "--days"
       - "{{ tpl .Values.cronJobs.maintenance.extraSettings.days $ }}"
+    extraFileMappings:
+      /galaxy/server/scripts/maintenance.sh:
+        tpl: true
+        content: |
+          {{ .Files.Get "files/source/maintenance.sh" }}
+      /galaxy/server/scripts/cleanup_datasets/cleanup_datasets.py:
+        tpl: true
+        content: |
+          {{ .Files.Get "files/source/cleanup_datasets.py" }}
+
   #- Remove files from the tmp directory that are older than the allowable wall time for a job
   tmpdir:
     schedule: "15 2 * * *"

From cf779636840176347aced3133fcde69faa6b0eca Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 28 Feb 2024 12:59:07 -0600
Subject: [PATCH 19/68] Start documenting cron jobs

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 3c150f37..e023b3de 100644
--- a/README.md
+++ b/README.md
@@ -417,6 +417,10 @@ 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.
 
+## Cron jobs
+
+Two Cron jobs are defined to clean up Galaxy's database and the `tmp` directory.  By default these
+jobs run at 02:05 (the database maintenance script) and 02:15 (`tmp` directyory cleanup). Users 
 ## Galaxy versions
 
 Some changes introduced in the chart sometimes rely on changes in the Galaxy

From 13e4f0bc4a6701b612aec883d095e2be271c3a0b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 8 Mar 2024 11:31:35 -0500
Subject: [PATCH 20/68] Make the galaxy.yml file available in a configmap for
 the maintenance cronjob

---
 galaxy/templates/configmap-galaxy.yaml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 galaxy/templates/configmap-galaxy.yaml

diff --git a/galaxy/templates/configmap-galaxy.yaml b/galaxy/templates/configmap-galaxy.yaml
new file mode 100644
index 00000000..e69de29b

From 27fd304e4d1090d8688bc267925c29c3f0086c42 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 8 Mar 2024 12:11:17 -0500
Subject: [PATCH 21/68] Update galaxy/values.yaml

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 galaxy/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 1fc25660..dc252c7e 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -267,7 +267,7 @@ extraEnv: []
   # - name: EXAMPLE_ENV
   #   value: MY_VALUE
 
-#- CronJobs to perform periodic maintenacne tasks
+#- CronJobs to perform periodic maintenance tasks
 cronJobs:
   #- Runs the maintenance.sh script to clean up the Galaxy database.
   maintenance:

From 42488ff883ed0ec00d80d7fd3fb9cf73a5c77a5c Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Sun, 10 Mar 2024 16:55:10 -0400
Subject: [PATCH 22/68] Add helper to calculate the postgres connection string

---
 galaxy/disabled/configmap-galaxy.yaml  | 9 +++++++++
 galaxy/templates/_helpers.tpl          | 7 +++++++
 galaxy/templates/configmap-galaxy.yaml | 0
 3 files changed, 16 insertions(+)
 create mode 100644 galaxy/disabled/configmap-galaxy.yaml
 delete mode 100644 galaxy/templates/configmap-galaxy.yaml

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/templates/_helpers.tpl b/galaxy/templates/_helpers.tpl
index 4d7bb779..2f817cae 100644
--- a/galaxy/templates/_helpers.tpl
+++ b/galaxy/templates/_helpers.tpl
@@ -79,6 +79,13 @@ Return the postgresql database name to use
 {{- 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-galaxy.yaml b/galaxy/templates/configmap-galaxy.yaml
deleted file mode 100644
index e69de29b..00000000

From 0fafea87f60fb9719e2e26491013a0148954a36a Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Sun, 10 Mar 2024 16:55:46 -0400
Subject: [PATCH 23/68] Add cron job documentation and remove Galaxy versions
 section

---
 README.md | 34 ++++++++++++++++++----------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index e023b3de..77480d43 100644
--- a/README.md
+++ b/README.md
@@ -269,6 +269,8 @@ 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.
@@ -420,22 +422,22 @@ by setting the desired values of the `webHandlers.replicaCount`,
 ## Cron jobs
 
 Two Cron jobs are defined to clean up Galaxy's database and the `tmp` directory.  By default these
-jobs run at 02:05 (the database maintenance script) and 02:15 (`tmp` directyory cleanup). Users 
-## Galaxy versions
-
-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`.
-
-
-| 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` |
+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
+```
+
+To disable a cron job after Galaxy has been deployed simply set the schedule to a date that
+can never occur such as midnight on Februrary 30th:
+
+
+```bash
+helm upgrade galaxy -n galaxy galaxy/galaxy --reuse-values --set cronJobs.maintenance.schedule="0 0 30 2 *"
+```
 
 ## Funding
 

From 497b5729c94691c8a4da4d31125c519a363432d6 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 12 Mar 2024 15:08:55 -0400
Subject: [PATCH 24/68] Add env definitions

---
 galaxy/templates/cronjob-maintenance.yaml | 55 ++++++++++++++++++-----
 1 file changed, 45 insertions(+), 10 deletions(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 954304a5..be71e35d 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -27,6 +27,15 @@ spec:
           - name: galaxy-cron-{{ $key }}
             image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
             imagePullPolicy: {{ $.Values.image.pullPolicy }}
+            {{- if or $cronjob.defaultEnv $cronjob.extraEnv }}
+            env:
+            {{- if $cronjob.defaultEnv }}
+            {{- include "galaxy.podEnvVars" $}}
+            {{- end }}
+            {{- if $cronjob.extraEnv }}
+            {{- $cronjob.extraEnv | toYaml | nindent 12 }}
+            {{- end }}
+            {{- end }}
             command:
             {{- range $cmd := $cronjob.command }}
               - {{ tpl $cmd $ | quote }}
@@ -40,7 +49,7 @@ spec:
             volumeMounts:
             - name: galaxy-data
               mountPath: {{ $.Values.persistence.mountPath }}
-            {{- range $key, $entry := $cronjob.extraFileMappings -}}
+            {{- range $key, $entry := $cronjob.extraFileMappings }}
             - name: {{ include "galaxy.getExtraFilesUniqueName" $key }}
               mountPath: {{ $key }}
               subPath: {{ include "galaxy.getFilenameFromPath" $key }}
@@ -53,15 +62,41 @@ spec:
             {{- 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) }}
+          {{- 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 }}
           {{- 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 }}
\ No newline at end of file

From da6a97a73a51e5fb625345326c1edb1e8df6a64b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 12 Mar 2024 15:11:04 -0400
Subject: [PATCH 25/68] Maintenace job should include default env vars

---
 galaxy/values.yaml | 23 +++++++----------------
 1 file changed, 7 insertions(+), 16 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index dc252c7e..36f80939 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -269,31 +269,22 @@ extraEnv: []
 
 #- CronJobs to perform periodic maintenance tasks
 cronJobs:
-  #- Runs the maintenance.sh script to clean up the Galaxy database.
+  #- Runs the maintenance.sh script to purge items in the Galaxy database that
+  #- have been flagged as deleted.
   maintenance:
     schedule: "5 2 * * *"
     extraSettings:
+      #- Purge items older than this.
       days: '7'
     securityContext:
       runAsUser: 0
+    defaultEnv: true
     command:
-      - "/bin/bash"
-      - "-c"
-    args:
       - "/galaxy/server/scripts/maintenance.sh"
+    args:
       - "--no-dry-run"
       - "--days"
       - "{{ tpl .Values.cronJobs.maintenance.extraSettings.days $ }}"
-    extraFileMappings:
-      /galaxy/server/scripts/maintenance.sh:
-        tpl: true
-        content: |
-          {{ .Files.Get "files/source/maintenance.sh" }}
-      /galaxy/server/scripts/cleanup_datasets/cleanup_datasets.py:
-        tpl: true
-        content: |
-          {{ .Files.Get "files/source/cleanup_datasets.py" }}
-
   #- Remove files from the tmp directory that are older than the allowable wall time for a job
   tmpdir:
     schedule: "15 2 * * *"
@@ -317,7 +308,6 @@ cronJobs:
 ingress:
   #- Should ingress be enabled. Defaults to `true`
   enabled: true
-  #-
   ingressClassName: nginx
   canary:
     enabled: true
@@ -490,7 +480,8 @@ 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}}"

From cdc2a989d5135e510798808036d9444cfa91c2c1 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 12 Mar 2024 17:14:05 -0400
Subject: [PATCH 26/68] Update galaxy/values.yaml

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 galaxy/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 36f80939..02eb18b2 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -289,7 +289,7 @@ cronJobs:
   tmpdir:
     schedule: "15 2 * * *"
     extraSettings:
-      last_modified: '{{ index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800 }}'
+      lastModified: '{{ index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800 }}'
     securityContext:
       runAsUser: 0
     command:

From 63bc997ec1ba41cdff7b0eb4f509b1c554c586c3 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 12 Mar 2024 17:16:28 -0400
Subject: [PATCH 27/68] Update galaxy/values.yaml

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 galaxy/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 02eb18b2..519e9a39 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -298,7 +298,7 @@ cronJobs:
       - "{{ .Values.persistence.mountPath }}/tmp"
       - "!"
       - "-newermt"
-      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.last_modified $ }} seconds ago"
+      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.lastModified $ }} seconds ago"
       - "-type"
       - "f"
       - "-exec"

From d96979a35cda1b6ff402cba3570a9ea6dfd08286 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 12 Mar 2024 18:34:16 -0400
Subject: [PATCH 28/68] Parameterize Docker image for cron jobs

---
 galaxy/templates/cronjob-maintenance.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index be71e35d..a5009841 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -25,7 +25,11 @@ spec:
           {{- end }}
           containers:
           - 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:

From 3af24cd85cf97acc0a1105607af037e225ce388a Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 13 Mar 2024 14:58:41 -0400
Subject: [PATCH 29/68] Allow mode (permissions) to be defined on
 extraFileMappings

---
 galaxy/templates/cronjob-maintenance.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index a5009841..c6366435 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -75,6 +75,9 @@ spec:
             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 }}

From b058b5e2ce1cec54148cccb68805fb755dc35890 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 13 Mar 2024 16:06:07 -0400
Subject: [PATCH 30/68] Add YAML document separators (triple dashes) to the
 start of yaml templates.

---
 galaxy/templates/configmap-cvmfs-fix.yaml         | 1 +
 galaxy/templates/configmap-extra-files.yaml       | 5 ++---
 galaxy/templates/configmap-galaxy-rules.yaml      | 1 +
 galaxy/templates/configmap-grafana-dashboard.yaml | 1 +
 galaxy/templates/configmap-nginx.yaml             | 1 +
 galaxy/templates/configs-galaxy.yaml              | 1 +
 galaxy/templates/cronjob-maintenance.yaml         | 1 +
 galaxy/templates/deployment-celery-beat.yaml      | 1 +
 galaxy/templates/deployment-celery.yaml           | 1 +
 galaxy/templates/deployment-job.yaml              | 2 +-
 galaxy/templates/deployment-metrics.yaml          | 1 +
 galaxy/templates/deployment-nginx.yaml            | 1 +
 galaxy/templates/deployment-tusd.yaml             | 1 +
 galaxy/templates/deployment-web.yaml              | 1 +
 galaxy/templates/deployment-workflow.yaml         | 1 +
 galaxy/templates/hook-cvmfs-fix.yaml              | 1 +
 galaxy/templates/ingress-activity-canary.yaml     | 3 ++-
 galaxy/templates/ingress-tusd.yaml                | 3 ++-
 galaxy/templates/ingress.yaml                     | 2 +-
 galaxy/templates/jobs-init.yaml                   | 1 +
 galaxy/templates/priorityclass-job.yaml           | 1 +
 galaxy/templates/pv-s3fs.yaml                     | 1 +
 galaxy/templates/pvc-galaxy.yaml                  | 2 +-
 galaxy/templates/pvc-refdata.yaml                 | 2 +-
 galaxy/templates/rabbitmqcluster.yaml             | 1 +
 galaxy/templates/rbac-job.yaml                    | 1 +
 galaxy/templates/secret-galaxy.yaml               | 1 +
 galaxy/templates/service-galaxy.yaml              | 1 +
 galaxy/templates/service-nginx.yaml               | 1 +
 galaxy/templates/service-tusd.yaml                | 1 +
 galaxy/templates/serviceaccount.yaml              | 1 +
 31 files changed, 34 insertions(+), 9 deletions(-)

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..80deecd5 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -1,3 +1,4 @@
+---
 apiVersion: batch/v1
 kind: CronJob
 metadata:
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 3f29b7b6..03637c43 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..a954ae77 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
+---
 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 3ee42943..5c0ed980 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:

From 3fe57237af05e77ff1619cda06d2ee0d49a27acf Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 13 Mar 2024 17:33:23 -0400
Subject: [PATCH 31/68] Add example cron job

---
 galaxy/values.yaml | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 519e9a39..cfe2bd4e 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -305,6 +305,50 @@ cronJobs:
       - "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

From 07fdbd4ba46e4e76172e8bae8a06174affc82683 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 13 Mar 2024 17:33:41 -0400
Subject: [PATCH 32/68] Additional documentation for cron jobs

---
 README.md | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 55 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 77480d43..4d5aebbc 100644
--- a/README.md
+++ b/README.md
@@ -421,7 +421,7 @@ by setting the desired values of the `webHandlers.replicaCount`,
 
 ## Cron jobs
 
-Two Cron jobs are defined to clean up Galaxy's database and the `tmp` directory.  By default these
+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:
 
@@ -430,7 +430,11 @@ 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 schedule to a date that
 can never occur such as midnight on Februrary 30th:
 
@@ -439,6 +443,55 @@ can never occur such as midnight on Februrary 30th:
 helm upgrade galaxy -n galaxy galaxy/galaxy --reuse-values --set cronJobs.maintenance.schedule="0 0 30 2 *"
 ```
 
+### 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 |
+|---|-------------------------------------------------------------------------------------------------------------------------------------------|----------|
+| 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.
+
+| 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**  | 
+
+
+See the `example` cron job included in the `values.yaml` file for a full example.
+
+
 ## Funding
 
 - _Version 3+_: Galaxy Project, Genomics Virtual Laboratory (GVL)

From b4cbdf6e76347f5f819ad197efa6cf3f58506f89 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 13 Mar 2024 21:56:49 -0400
Subject: [PATCH 33/68] Comment out the example cron job. Examples should not
 add arbitrary code to clusters.

---
 galaxy/values.yaml | 86 +++++++++++++++++++++++-----------------------
 1 file changed, 43 insertions(+), 43 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index cfe2bd4e..fdc57bab 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -305,49 +305,49 @@ cronJobs:
       - "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
+#  #- 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`

From db82ef00fc90b406e326f6848ea4c2940830cbf4 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Sun, 17 Mar 2024 15:00:24 -0400
Subject: [PATCH 34/68] Run extraEnv values through the template engine

---
 galaxy/templates/cronjob-maintenance.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index c6366435..25a069b6 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -37,7 +37,10 @@ spec:
             {{- include "galaxy.podEnvVars" $}}
             {{- end }}
             {{- if $cronjob.extraEnv }}
-            {{- $cronjob.extraEnv | toYaml | nindent 12 }}
+            {{- range $env := $cronjob.extraEnv }}
+            - name: {{ $env.name }}
+              value: {{ tpl $env.value $ | quote }}
+            {{- end }}
             {{- end }}
             {{- end }}
             command:

From 859c6b7c31949feab84c6c91acaf1d1f2838d30c Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Thu, 21 Mar 2024 12:41:53 -0400
Subject: [PATCH 35/68] Run tests with 1.28, and add missing tool versions to
 sanitize allowlist

---
 .github/workflows/test.yaml |  2 +-
 galaxy/values.yaml          | 14 ++++++++++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index bbde0299..324e7ae7 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
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 4c2ebae0..94c606b9 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -498,21 +498,31 @@ 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
   build_sites.yml:
     - type: ucsc

From c36336d2b8a69ea0e2645f2a7194ae115adade4b Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Tue, 16 Apr 2024 20:55:46 +0000
Subject: [PATCH 36/68] Automatic Version Bumping from 5.9.0 to 5.10.0

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 572b68bb..f446ec96 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.9.0
+version: 5.10.0
 appVersion: "23.1"
 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

From e81042cdb9751bc70d8f75c368dd765164a26ba6 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Tue, 16 Apr 2024 16:09:13 -0500
Subject: [PATCH 37/68] Add plotly tools to allow list

---
 galaxy/values.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 94c606b9..710fdbb8 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -524,6 +524,9 @@ configs:
     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}}"

From dfceb29c93dbd42d90cae0fdea103944fdd2f5ea Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 17 Apr 2024 11:09:28 -0400
Subject: [PATCH 38/68] Add checkout set to the tag-and-release step.

---
 .github/workflows/packaging.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index 7436a068..e168fe5b 100644
--- a/.github/workflows/packaging.yml
+++ b/.github/workflows/packaging.yml
@@ -56,6 +56,9 @@ jobs:
       && contains(needs.*.result, 'success')
       && !contains(needs.*.result, 'failure')
     steps:
+      - uses: actions/checkout@v2
+        with:
+           persist-credentials: false
       - name: Tag and release
         run: |
           version=v$(cat galaxy/Chart.yaml | grep ^version: | awk '{print $2}')

From 7236270bd6c064e68e4374f54181969193dc80f8 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 17 Apr 2024 11:58:28 -0400
Subject: [PATCH 39/68] Update .github/workflows/packaging.yml

Use latest version of the checkout action.

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 .github/workflows/packaging.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index e168fe5b..ae7191ac 100644
--- a/.github/workflows/packaging.yml
+++ b/.github/workflows/packaging.yml
@@ -56,7 +56,7 @@ jobs:
       && contains(needs.*.result, 'success')
       && !contains(needs.*.result, 'failure')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
            persist-credentials: false
       - name: Tag and release

From 576807e64a0f9b1546fd5137d3a94df5468802f8 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 17 Apr 2024 12:06:51 -0400
Subject: [PATCH 40/68] Update all checkout actions to v4

---
 .github/workflows/packaging.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index ae7191ac..a1bb5195 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

From 60a4ecc93dcbe79227e28de48a77a5268af60525 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 17 Apr 2024 18:44:59 +0000
Subject: [PATCH 41/68] Automatic Version Bumping from 5.10.0 to 5.10.1

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index f446ec96..04d48e48 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.10.0
+version: 5.10.1
 appVersion: "23.1"
 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

From ba6afdd7928285d0c2bc2c3146ad4112a5e7ce65 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 17 Apr 2024 18:46:54 +0000
Subject: [PATCH 42/68] Automatic Version Bumping from 5.10.1 to 5.11.0

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 04d48e48..aad942ce 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.10.1
+version: 5.11.0
 appVersion: "23.1"
 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

From 9df267e76c161c6fcf7787ebce3fc2901fe01d2b Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 17 Apr 2024 18:59:05 -0400
Subject: [PATCH 43/68] Set user.name and user.email for the GitHub bot

---
 .github/workflows/packaging.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index a1bb5195..463a18ea 100644
--- a/.github/workflows/packaging.yml
+++ b/.github/workflows/packaging.yml
@@ -61,6 +61,8 @@ jobs:
            persist-credentials: false
       - 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

From 14f190de57584bc19a64bbfaf6eb772544354bef Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 17 Apr 2024 20:03:35 -0400
Subject: [PATCH 44/68] Add newline to the end of the file.

---
 galaxy/templates/cronjob-maintenance.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 25a069b6..0ea57a5e 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -109,4 +109,4 @@ data:
 {{- end }}
 {{- end }}
 
-{{- end }}
\ No newline at end of file
+{{- end }}

From 2e32eac21894a6b4cd3ff3d09d33f470e100af68 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Thu, 18 Apr 2024 14:58:38 +0000
Subject: [PATCH 45/68] Automatic Version Bumping from 5.11.0 to 5.12.0

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index aad942ce..fa86b990 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.11.0
+version: 5.12.0
 appVersion: "23.1"
 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

From 7e61ac16a2b3f98d0ce1cad6794acfc73adffb17 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Thu, 18 Apr 2024 11:50:40 -0400
Subject: [PATCH 46/68] Add enabled flag to the actions

---
 galaxy/templates/cronjob-maintenance.yaml | 4 ++++
 galaxy/values.yaml                        | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 0ea57a5e..6b89135e 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -7,7 +7,11 @@ metadata:
   labels:
     {{- include "galaxy.labels" $ | nindent 4 }}
 spec:
+  {{- if $cronjob.enabled }}
   schedule: {{ $cronjob.schedule | quote }}
+  {{- else }}
+  schedule: "0 0 30 2 *"
+  {{- end }}
   jobTemplate:
     spec:
       template:
diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index ba5e6f54..41700f5b 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -272,6 +272,7 @@ 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.
@@ -287,6 +288,7 @@ cronJobs:
       - "{{ 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 }}'

From bbdbdb9c18913146f935f05d090b0f67292516af Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 19 Apr 2024 16:19:09 -0400
Subject: [PATCH 47/68] Update galaxy/templates/cronjob-maintenance.yaml

Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
---
 galaxy/templates/cronjob-maintenance.yaml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/galaxy/templates/cronjob-maintenance.yaml b/galaxy/templates/cronjob-maintenance.yaml
index 6b89135e..d020b4f7 100644
--- a/galaxy/templates/cronjob-maintenance.yaml
+++ b/galaxy/templates/cronjob-maintenance.yaml
@@ -10,6 +10,8 @@ spec:
   {{- 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:

From 68be5dfc320d76a9e74952c5d4770bff27b9d8f1 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Thu, 18 Apr 2024 00:25:35 +0530
Subject: [PATCH 48/68] Update README.md

---
 README.md | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 615e2b7e..db1e3df1 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
@@ -495,12 +495,3 @@ The following fields can be specified for each file.
 See the `example` cron job included in the `values.yaml` file for a full example.
 
 
-## Funding
-
-- _Version 3+_: Galaxy Project, Genomics Virtual Laboratory (GVL)
-
-- _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.

From 17e8292b0d692b3a062a5aced5aa801267ebc3ed Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 23 Apr 2024 16:53:56 -0400
Subject: [PATCH 49/68] Document enabled flag for cron jobs

---
 README.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 615e2b7e..5545aac1 100644
--- a/README.md
+++ b/README.md
@@ -438,12 +438,11 @@ or by specifying the `schedule` on the command line when instaling Galaxy:
 # 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 schedule to a date that
-can never occur such as midnight on Februrary 30th:
+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.schedule="0 0 30 2 *"
+helm upgrade galaxy -n galaxy galaxy/galaxy --reuse-values --set cronJobs.maintenance.enabled=false
 ```
 
 ### Run a CronJob manually
@@ -464,6 +463,7 @@ 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       |
@@ -471,7 +471,7 @@ The following fields can be specified when defining cron jobs.
 | 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 |
+| extraFileMappings | Allow arbitrary files to be mounted from config maps | No       |
 
 ### Notes
 

From 7fe918b8f9e63f36130e785bad91b6e1db5c9b98 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Tue, 23 Apr 2024 17:01:41 -0400
Subject: [PATCH 50/68] Persist credentials and set GH_TOKEN for the GitHub
 command line tool

---
 .github/workflows/packaging.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index 463a18ea..dbcc3a96 100644
--- a/.github/workflows/packaging.yml
+++ b/.github/workflows/packaging.yml
@@ -51,14 +51,14 @@ 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:
-           persist-credentials: false
       - name: Tag and release
         run: |
           git config user.name "GitHub Actions Bot"

From c16ea126cfd88780779a8ba7a006397d3eda9618 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 24 Apr 2024 04:52:37 +0000
Subject: [PATCH 51/68] Automatic Version Bumping from 5.12.0 to 5.12.1

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index fa86b990..89882b2e 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.12.0
+version: 5.12.1
 appVersion: "23.1"
 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

From d918841e7cfc8f2507df9eb4ce5635b5b3618188 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 24 Apr 2024 04:57:55 +0000
Subject: [PATCH 52/68] Automatic Version Bumping from 5.12.1 to 5.13.0

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 89882b2e..d51fa067 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.12.1
+version: 5.13.0
 appVersion: "23.1"
 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

From 431c683dd76c73b2ef5f1194fddadf9b9fc32729 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 26 Apr 2024 09:35:06 -0400
Subject: [PATCH 53/68] Ensure tag-and-release checks out the latest commits
 make by the helm-ci action.

---
 .github/workflows/packaging.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml
index dbcc3a96..9fe495e6 100644
--- a/.github/workflows/packaging.yml
+++ b/.github/workflows/packaging.yml
@@ -59,6 +59,8 @@ jobs:
       && !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"

From ef74d1ee6baff0a3a1955649213676dff2718cb0 Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Wed, 8 May 2024 11:16:21 -0400
Subject: [PATCH 54/68] Update Galaxy (to 24.0.2) and CVMFS-CSI

---
 galaxy/Chart.yaml  | 4 ++--
 galaxy/values.yaml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index d51fa067..d6ada580 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -2,7 +2,7 @@ apiVersion: v2
 name: galaxy
 type: application
 version: 5.13.0
-appVersion: "23.1"
+appVersion: "24.0.2"
 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/values.yaml b/galaxy/values.yaml
index 41700f5b..d0ce480e 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -10,7 +10,7 @@ image:
   #- Repository containing the Galaxy image.
   repository: quay.io/galaxyproject/galaxy-min
   #- Galaxy Docker image tag (generally corresponds to the desired Galaxy version)
-  tag: "23.1"  # Value must be quoted
+  tag: "24.0.2"  # Value must be quoted
   #-  Galaxy image [pull policy](https://kubernetes.io/docs/concepts/configuration/overview/#container-images)
   pullPolicy: IfNotPresent
 

From b6ca6621f4ae37c39c4b10c6823103b3ee07a611 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 8 May 2024 18:07:51 +0000
Subject: [PATCH 55/68] Automatic Version Bumping from 5.13.0 to 5.14.0

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index d6ada580..6c6f0442 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.13.0
+version: 5.14.0
 appVersion: "24.0.2"
 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

From 5f5c1bd9263e682d5fe1fb494d1f57c2ac4beceb Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 10 May 2024 12:05:09 -0400
Subject: [PATCH 56/68] Allow data volume mounts to be writable

---
 galaxy/values.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index d0ce480e..20ea96bf 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -467,7 +467,7 @@ configs:
         load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
         k8s_use_service_account: true
         k8s_data_volume_claim: |-
-          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}:r
+          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
         k8s_working_volume_claim: |-
           {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
         k8s_persistent_volume_claims: |-

From 694ce4dc71136e2e793f33ace4697e6764ba5ed9 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 10 May 2024 12:06:31 -0400
Subject: [PATCH 57/68] Add shed_tools directory to the list of persistent
 volume mounts

---
 galaxy/values.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 20ea96bf..5df70174 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -474,7 +474,8 @@ configs:
           {{ 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:r,
-          {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools:r
+          {{- 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:r
           {{- end -}}

From 8f312ab3d8666a5a2b82b834e8d0a0ee9a2cbdf8 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Fri, 31 May 2024 10:51:54 -0400
Subject: [PATCH 58/68] Add test values

---
 galaxy/values.yaml | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 5df70174..0bfc9d72 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -466,6 +466,28 @@ configs:
       k8s:
         load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
         k8s_use_service_account: true
+#        k8s_persistent_volume_claims: |-
+#          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
+#          {{- if .Values.refdata.enabled -}}
+#          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org
+#          {{- end -}}
+#          {{- if .Values.setupJob.downloadToolConfs.enabled -}}
+#          ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}
+#          {{- end -}}
+#          {{- if .Values.extraVolumes -}}
+#          {{- template "galaxy.extra_pvc_mounts" . -}}
+#          {{- end }}
+#          {{- template "galaxy.pvcname" . -}}/celery-beat-schedule:{{ .Values.persistence.mountPath -}}/celery-beat-schedule,
+#          {{- template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache,
+#          {{- template "galaxy.pvcname" . -}}/cvmfsclone:{{ .Values.persistence.mountPath -}}/cvmfsclone,
+#          {{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps,
+#          {{- template "galaxy.pvcname" . -}}/jobs_directory:{{ .Values.persistence.mountPath -}}/jobs_directory
+#          {{- template "galaxy.pvcname" . -}}/objects:{{ .Values.persistence.mountPath -}}/objects,
+#          {{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index
+#          {{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache
+#          {{- template "galaxy.pvcname" . -}}/jobs_directory:{{ .Values.persistence.mountPath -}}/jobs_directory,
+
+
         k8s_data_volume_claim: |-
           {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
         k8s_working_volume_claim: |-
@@ -473,9 +495,10 @@ configs:
         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:r,
+          {{- 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
+          {{- template "galaxy.pvcname" . -}}/shed_tools:{{ .Values.persistence.mountPath -}}/shed_tools:r,
+          {{- template "galaxy.pvcname" . -}}/objects:{{ .Values.persistence.mountPath -}}/objects
           {{- if .Values.refdata.enabled -}}
           ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:r
           {{- end -}}

From 628254075db0cea31f457b97cad2aed0e66a4509 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 5 Jun 2024 20:40:26 -0400
Subject: [PATCH 59/68] Add shed_tools and objects as read-only

---
 galaxy/values.yaml | 26 ++------------------------
 1 file changed, 2 insertions(+), 24 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index 0bfc9d72..c07036bf 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -466,28 +466,6 @@ configs:
       k8s:
         load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
         k8s_use_service_account: true
-#        k8s_persistent_volume_claims: |-
-#          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
-#          {{- if .Values.refdata.enabled -}}
-#          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org
-#          {{- end -}}
-#          {{- if .Values.setupJob.downloadToolConfs.enabled -}}
-#          ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}
-#          {{- end -}}
-#          {{- if .Values.extraVolumes -}}
-#          {{- template "galaxy.extra_pvc_mounts" . -}}
-#          {{- end }}
-#          {{- template "galaxy.pvcname" . -}}/celery-beat-schedule:{{ .Values.persistence.mountPath -}}/celery-beat-schedule,
-#          {{- template "galaxy.pvcname" . -}}/cache:{{ .Values.persistence.mountPath -}}/cache,
-#          {{- template "galaxy.pvcname" . -}}/cvmfsclone:{{ .Values.persistence.mountPath -}}/cvmfsclone,
-#          {{- template "galaxy.pvcname" . -}}/deps:{{ .Values.persistence.mountPath -}}/deps,
-#          {{- template "galaxy.pvcname" . -}}/jobs_directory:{{ .Values.persistence.mountPath -}}/jobs_directory
-#          {{- template "galaxy.pvcname" . -}}/objects:{{ .Values.persistence.mountPath -}}/objects,
-#          {{- template "galaxy.pvcname" . -}}/tool_search_index:{{ .Values.persistence.mountPath -}}/tool_search_index
-#          {{- template "galaxy.pvcname" . -}}/object_store_cache:{{ .Values.persistence.mountPath -}}/object_store_cache
-#          {{- template "galaxy.pvcname" . -}}/jobs_directory:{{ .Values.persistence.mountPath -}}/jobs_directory,
-
-
         k8s_data_volume_claim: |-
           {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
         k8s_working_volume_claim: |-
@@ -497,8 +475,8 @@ configs:
           {{- 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,
-          {{- template "galaxy.pvcname" . -}}/objects:{{ .Values.persistence.mountPath -}}/objects
+          {{- template "galaxy.pvcname" . -}}/objects:{{ .Values.persistence.mountPath -}}/objects: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:r
           {{- end -}}

From 15fa77d17ed57f376da9a5aabeecdb52d6df64c3 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 10 Jun 2024 17:12:26 +0000
Subject: [PATCH 60/68] Automatic Version Bumping from 5.14.0 to 5.14.1

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 6c6f0442..ea9993f8 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.14.0
+version: 5.14.1
 appVersion: "24.0.2"
 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

From b50c171d02689cffae8ff24bb2aa9d2c72c4a484 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Thu, 13 Jun 2024 03:16:45 +0000
Subject: [PATCH 61/68] Automatic Version Bumping from 5.14.1 to 5.14.2

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index ea9993f8..880f6153 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.14.1
+version: 5.14.2
 appVersion: "24.0.2"
 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

From 5481d672288be1e6034b13854c15d8425a47750c Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Sat, 29 Jun 2024 13:26:02 +0200
Subject: [PATCH 62/68] Don't give read permission to the entire objects
 directory

---
 galaxy/values.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
index c07036bf..6da949fd 100644
--- a/galaxy/values.yaml
+++ b/galaxy/values.yaml
@@ -10,7 +10,7 @@ image:
   #- Repository containing the Galaxy image.
   repository: quay.io/galaxyproject/galaxy-min
   #- Galaxy Docker image tag (generally corresponds to the desired Galaxy version)
-  tag: "24.0.2"  # 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
 
@@ -475,7 +475,6 @@ configs:
           {{- 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" . -}}/objects:{{ .Values.persistence.mountPath -}}/objects: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:r

From b8c9649e8cfbbc8835460876f3b7e0cb0a83d3e1 Mon Sep 17 00:00:00 2001
From: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
Date: Sun, 30 Jun 2024 00:17:12 +0530
Subject: [PATCH 63/68] Add instructions for using dnsmasq on Linux

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 3eef49ff..fc7d6871 100644
--- a/README.md
+++ b/README.md
@@ -395,6 +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

From 382f839f937d934c68409ace7db55fe543fad64c Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Fri, 5 Jul 2024 16:24:38 +0000
Subject: [PATCH 64/68] Automatic Version Bumping from 5.14.2 to 5.14.3

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 880f6153..bac329c0 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.14.2
+version: 5.14.3
 appVersion: "24.0.2"
 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

From 8d97fa1fee5a754ec8aa73e0cd8034e9ba388cfc Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jul 2024 10:27:30 -0400
Subject: [PATCH 65/68] Check that the appVersion matches version returned by
 /api/version

---
 .github/workflows/test.yaml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index 324e7ae7..d7f156ea 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -64,3 +64,21 @@ jobs:
       - name: Print workflow handler log
         run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-workflow[^ ]*')"
         if: always()
+      - name: Print service info
+        run: kubectl get svc -n galaxy
+        if: always()
+      - name: Print nginx service info
+        run: kubectl describe svc -n galaxy galaxy-nginx
+        if: always()
+      - name: Check appVersion
+        if: always()
+        run: |
+          appVersion=$(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  

From a9f1e3ac6174c821a53d877b3493dea70462d6e0 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jul 2024 11:43:48 -0400
Subject: [PATCH 66/68] Update appVersion in the Chart.yaml

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index bac329c0..762af1b4 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -2,7 +2,7 @@ apiVersion: v2
 name: galaxy
 type: application
 version: 5.14.3
-appVersion: "24.0.2"
+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:

From a88a615f7eb6aa131793925681ea922c1881d1a4 Mon Sep 17 00:00:00 2001
From: Keith Suderman <suderman@jhu.edu>
Date: Wed, 10 Jul 2024 14:15:18 -0400
Subject: [PATCH 67/68] Print output from kubectl as part of the appVersion
 test

---
 .github/workflows/test.yaml | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
index d7f156ea..db7f47f9 100644
--- a/.github/workflows/test.yaml
+++ b/.github/workflows/test.yaml
@@ -64,15 +64,11 @@ jobs:
       - name: Print workflow handler log
         run: bash -c "kubectl logs -n galaxy $(kubectl -n galaxy get pods | grep -o '[^ ]*galaxy-workflow[^ ]*')"
         if: always()
-      - name: Print service info
-        run: kubectl get svc -n galaxy
-        if: always()
-      - name: Print nginx service info
-        run: kubectl describe svc -n galaxy galaxy-nginx
-        if: always()
       - name: Check appVersion
         if: always()
         run: |
+          kubectl get svc -n galaxy
+          kubectl describe svc -n galaxy galaxy-nginx
           appVersion=$(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"

From 91e11e0dfbaae3f48e04636eeaf42a7ca40cd890 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 10 Jul 2024 18:19:14 +0000
Subject: [PATCH 68/68] Automatic Version Bumping from 5.14.3 to 5.15.0

---
 galaxy/Chart.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/galaxy/Chart.yaml b/galaxy/Chart.yaml
index 762af1b4..a9fa0fc4 100644
--- a/galaxy/Chart.yaml
+++ b/galaxy/Chart.yaml
@@ -1,7 +1,7 @@
 apiVersion: v2
 name: galaxy
 type: application
-version: 5.14.3
+version: 5.15.0
 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