From ea30dee5d29a87218f0593294e0169786c328b72 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <mahmoudalexandru@gmail.com>
Date: Mon, 2 May 2022 15:53:12 -0400
Subject: [PATCH 1/4] Add libraries to init container

---
 bioconductor/templates/deployment.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/bioconductor/templates/deployment.yaml b/bioconductor/templates/deployment.yaml
index 9c1a5ef..8524b59 100644
--- a/bioconductor/templates/deployment.yaml
+++ b/bioconductor/templates/deployment.yaml
@@ -33,6 +33,10 @@ spec:
               subPath: {{ $entry.fileName }}
             {{- end -}}
             {{- end }}
+            {{- if and .Values.libraries.persistence.enabled .Values.libraries.persistence.separateClaim.enabled }}
+            - name: libraries
+              mountPath: {{.Values.libraries.persistence.separateClaim.mountPath}}
+            {{- end }}
             - name: rstudio-data
               mountPath: {{.Values.persistence.mountPath}}
               subPath: rstudio
@@ -116,4 +120,4 @@ spec:
         {{- end }}
         {{- if .Values.extraVolumes }}
         {{- .Values.extraVolumes | toYaml | nindent 8 }}
-        {{- end }}
\ No newline at end of file
+        {{- end }}

From 4266c7709bd3d98275ca0974b47ab9cf1ab2482a Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <mahmoudalexandru@gmail.com>
Date: Mon, 2 May 2022 16:06:01 -0400
Subject: [PATCH 2/4] Remove separate claim from init container

---
 bioconductor/templates/deployment.yaml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/bioconductor/templates/deployment.yaml b/bioconductor/templates/deployment.yaml
index 8524b59..a555030 100644
--- a/bioconductor/templates/deployment.yaml
+++ b/bioconductor/templates/deployment.yaml
@@ -75,10 +75,6 @@ spec:
               subPath: {{ $entry.fileName }}
             {{- end -}}
             {{- end }}
-            {{- if and .Values.libraries.persistence.enabled .Values.libraries.persistence.separateClaim.enabled }}
-            - name: libraries
-              mountPath: {{.Values.libraries.persistence.separateClaim.mountPath}}
-            {{- end }}
             - name: rstudio-data
               mountPath: {{.Values.persistence.mountPath}}
               subPath: rstudio

From b4f66090ee90d90a8ca9241fda9ed16d2e061778 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <mahmoudalexandru@gmail.com>
Date: Mon, 2 May 2022 16:06:37 -0400
Subject: [PATCH 3/4] Flip helper init command

---
 bioconductor/templates/_helpers.tpl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bioconductor/templates/_helpers.tpl b/bioconductor/templates/_helpers.tpl
index fa98e87..98dd453 100644
--- a/bioconductor/templates/_helpers.tpl
+++ b/bioconductor/templates/_helpers.tpl
@@ -88,10 +88,10 @@ Return which PVC to use for libraries
 Creates the bash command for the init containers used to place files and change permissions in the rstudio pods
 */}}
 {{- define "bioconductor.init-container-commands" -}}
-cp -anrL /opt/configs/readonly/rstudio/ /home/;
-chown -R rstudio:rstudio /home/rstudio;
 {{- if and .Values.libraries.persistence.enabled (not .Values.libraries.persistence.separateClaim.enabled) }}
 mkdir -p {{.Values.persistence.mountPath}}/persisted-library/R;
 {{- end }}
+cp -anrL /opt/configs/readonly/rstudio/ /home/;
+chown -R rstudio:rstudio /home/rstudio;
 {{- end -}}
 

From d04a2e5dc9809f1405ab998ad5500d3952f54699 Mon Sep 17 00:00:00 2001
From: Alexandru Mahmoud <mahmoudalexandru@gmail.com>
Date: Mon, 2 May 2022 16:16:26 -0400
Subject: [PATCH 4/4] Removed wrong side

---
 bioconductor/templates/deployment.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/bioconductor/templates/deployment.yaml b/bioconductor/templates/deployment.yaml
index a555030..f1f5818 100644
--- a/bioconductor/templates/deployment.yaml
+++ b/bioconductor/templates/deployment.yaml
@@ -33,10 +33,6 @@ spec:
               subPath: {{ $entry.fileName }}
             {{- end -}}
             {{- end }}
-            {{- if and .Values.libraries.persistence.enabled .Values.libraries.persistence.separateClaim.enabled }}
-            - name: libraries
-              mountPath: {{.Values.libraries.persistence.separateClaim.mountPath}}
-            {{- end }}
             - name: rstudio-data
               mountPath: {{.Values.persistence.mountPath}}
               subPath: rstudio
@@ -75,6 +71,10 @@ spec:
               subPath: {{ $entry.fileName }}
             {{- end -}}
             {{- end }}
+            {{- if and .Values.libraries.persistence.enabled .Values.libraries.persistence.separateClaim.enabled }}
+            - name: libraries
+              mountPath: {{.Values.libraries.persistence.separateClaim.mountPath}}
+            {{- end }}
             - name: rstudio-data
               mountPath: {{.Values.persistence.mountPath}}
               subPath: rstudio