Use args instead of command as entrypoint has changed in galaxyprojec…

…t/galaxy#12373
galaxyproject · Sep 8, 2021 · 65f8d92 · 65f8d92
1 parent 1123299
commit 65f8d92
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Showing 5 changed files with 11 additions and 14 deletions.
diff --git a/galaxy/templates/deployment-job.yaml b/galaxy/templates/deployment-job.yaml
@@ -44,7 +44,7 @@ spec:
         - name: {{ $.Chart.Name }}-wait-db
           image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}"
           imagePullPolicy: {{ $.Values.image.pullPolicy }}
-          command: ['sh', '-c', '{{ include "galaxy.init-container-wait-command" $ }} sleep {{ $.Values.jobHandlers.startupDelay }};']
+          args: ['sh', '-c', '{{ include "galaxy.init-container-wait-command" $ }} sleep {{ $.Values.jobHandlers.startupDelay }};']
           volumeMounts:
             - name: galaxy-data
               mountPath: /galaxy/server/config/mutable/
@@ -67,13 +67,12 @@ spec:
                 fieldRef:
                   fieldPath: metadata.name
           {{ include "galaxy.podEnvVars" $ }}
-          command: [
+          args: [
             'sh', '-c',
             '{{- if $.Values.extraInitCommands -}}
              {{- tpl $.Values.extraInitCommands $ | nindent 13 -}};
              {{- end -}}
              python /galaxy/server/scripts/galaxy-main -c /galaxy/server/config/galaxy.yml --server-name job_handler_{{ $handler_num }} --attach-to-pool job-handlers']
-          args: []
           {{- if $.Values.jobHandlers.startupProbe.enabled }}
           startupProbe:
             exec:

diff --git a/galaxy/templates/deployment-web.yaml b/galaxy/templates/deployment-web.yaml
@@ -41,7 +41,7 @@ spec:
         - name: {{ .Chart.Name }}-wait-db
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
-          command: ['sh', '-c', '{{ include "galaxy.init-container-wait-command" . }} sleep {{ .Values.webHandlers.startupDelay }};']
+          args: ['sh', '-c', '{{ include "galaxy.init-container-wait-command" . }} sleep {{ .Values.webHandlers.startupDelay }};']
           volumeMounts:
             - name: galaxy-data
               mountPath: /galaxy/server/config/mutable/
@@ -67,13 +67,12 @@ spec:
               protocol: TCP
           env:
           {{ include "galaxy.podEnvVars" . }}
-          command: [
+          args: [
             'sh', '-c',
             '{{- if .Values.extraInitCommands -}}
              {{- tpl .Values.extraInitCommands $ | nindent 13 }};
              {{- end -}}
              /galaxy/server/.venv/bin/uwsgi --yaml /galaxy/server/config/uwsgi.yml --set galaxy_config_file=/galaxy/server/config/galaxy.yml']
-          args: []
           {{- if .Values.webHandlers.startupProbe.enabled }}
           startupProbe:
             httpGet:

diff --git a/galaxy/templates/deployment-workflow.yaml b/galaxy/templates/deployment-workflow.yaml
@@ -41,7 +41,7 @@ spec:
         - name: {{ .Chart.Name }}-wait-db
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
-          command: ['sh', '-c', '{{ include "galaxy.init-container-wait-command" . }} sleep {{ .Values.workflowHandlers.startupDelay }};']
+          args: ['sh', '-c', '{{ include "galaxy.init-container-wait-command" . }} sleep {{ .Values.workflowHandlers.startupDelay }};']
           volumeMounts:
             - name: galaxy-data
               mountPath: /galaxy/server/config/mutable/
@@ -64,13 +64,12 @@ spec:
                 fieldRef:
                   fieldPath: metadata.name
           {{ include "galaxy.podEnvVars" . }}
-          command: [
+          args: [
             'sh', '-c',
             '{{- if .Values.extraInitCommands -}}
              {{- tpl .Values.extraInitCommands $ | nindent 13 -}};
              {{- end -}}
              python /galaxy/server/scripts/galaxy-main -c /galaxy/server/config/galaxy.yml --server-name workflow_scheduler0']
-          args: []
           {{- if .Values.workflowHandlers.startupProbe.enabled }}
           startupProbe:
             exec:

diff --git a/galaxy/templates/jobs-init.yaml b/galaxy/templates/jobs-init.yaml
@@ -38,7 +38,7 @@ spec:
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           {{- if .Values.initJob.createDatabase }}
-          command:
+          args:
             - 'sh'
             - '-c'
             - >
@@ -47,7 +47,7 @@ spec:
                 else (/galaxy/server/create_db.sh && echo "Done" > /galaxy/server/config/mutable/db_init_done_{{.Release.Revision}};);
               fi;
           {{- else }}
-          command:
+          args:
             - 'sh'
             - '-c'
             - '/galaxy/server/manage_db.sh upgrade && echo "Done" > /galaxy/server/config/mutable/db_init_done_{{.Release.Revision}};'
@@ -160,7 +160,7 @@ spec:
         - name: {{ .Chart.Name }}-init-mounts
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
-          command: ['sh', '-c', {{ include "galaxy.init-container-commands" . | squote }}]
+          args: ['sh', '-c', {{ include "galaxy.init-container-commands" . | squote }}]
           volumeMounts:
             {{- range $key, $entry := .Values.extraFileMappings -}}
             {{- if $entry.applyToWeb }}

diff --git a/galaxy/values.yaml b/galaxy/values.yaml
@@ -158,7 +158,7 @@ extraInitContainers: []
 #     applyToWeb: true
 #     applyToWorkflow: true
 #     image: "{{.Values.image.repository}}:{{.Values.image.tag}}"
-#     command: ['sh', '-c', 'cp "/galaxy/server/config/job_conf.xml.sample_advanced" {{.Values.persistence.mountPath}}/']
+#     args: ['sh', '-c', 'cp "/galaxy/server/config/job_conf.xml.sample_advanced" {{.Values.persistence.mountPath}}/']
 #     volumeMounts:
 #       - name: galaxy-data
 #         mountPath: "{{.Values.persistence.mountPath}}"
@@ -167,7 +167,7 @@ extraInitContainers: []
 #     applyToWeb: false
 #     applyToWorkflow: true
 #     image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
-#     command: ['sh', '-c', 'cp "/galaxy/server/config/galaxy.yml" {{.Values.persistence.mountPath}}/']
+#     args: ['sh', '-c', 'cp "/galaxy/server/config/galaxy.yml" {{.Values.persistence.mountPath}}/']
 #     volumeMounts:
 #       - name: galaxy-data
 #         mountPath: "{{.Values.persistence.mountPath}}"