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 1/3] 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 2/3] 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 3/3] 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 -}}