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Updating AnVIL branch to latest Galaxy Helm
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| --- | ||
| apiVersion: v1 | ||
| kind: ConfigMap | ||
| metadata: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| --- | ||
| apiVersion: v1 | ||
| kind: ConfigMap | ||
| metadata: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,5 @@ | ||
| {{- if .Values.influxdb.enabled }} | ||
| --- | ||
| apiVersion: v1 | ||
| kind: ConfigMap | ||
| metadata: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| --- | ||
| apiVersion: v1 | ||
| kind: ConfigMap | ||
| metadata: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| --- | ||
| apiVersion: v1 | ||
| metadata: | ||
| name: {{ include "galaxy.fullname" . }}-configs | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,47 +1,118 @@ | ||
| {{ range $key, $cronjob := .Values.cronJobs }} | ||
| --- | ||
| apiVersion: batch/v1 | ||
| kind: CronJob | ||
| metadata: | ||
| name: {{ include "galaxy.fullname" . }}-maintenance | ||
| name: {{ include "galaxy.fullname" $ }}-cron-{{ $key }} | ||
| labels: | ||
| {{- include "galaxy.labels" . | nindent 4 }} | ||
| {{- include "galaxy.labels" $ | nindent 4 }} | ||
| spec: | ||
| schedule: "0 2 * * *" | ||
| {{- if $cronjob.enabled }} | ||
| schedule: {{ $cronjob.schedule | quote }} | ||
| {{- else }} | ||
| # Set an impossible date so that the cronjob is still defined, but effectively disabled. | ||
| # This will allow the cronjob to be run manually if needed. | ||
| schedule: "0 0 30 2 *" | ||
| {{- end }} | ||
| jobTemplate: | ||
| spec: | ||
| template: | ||
| spec: | ||
| {{- if $cronjob.securityContext }} | ||
| securityContext: | ||
| {{- toYaml .Values.securityContext | nindent 12 }} | ||
| {{- with .Values.nodeSelector }} | ||
| {{- toYaml $cronjob.securityContext | nindent 12 }} | ||
| {{- end}} | ||
| {{- if $cronjob.nodeSelector }} | ||
| nodeSelector: | ||
| {{- toYaml . | nindent 16 }} | ||
| {{- toYaml $cronjob.nodeSelector | nindent 12 }} | ||
| {{- else if $.Values.nodeSelector }} | ||
| nodeSelector: | ||
| {{- toYaml $.Values.nodeSelector | nindent 12 }} | ||
| {{- end }} | ||
| containers: | ||
| - name: galaxy-maintenance | ||
| image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}" | ||
| imagePullPolicy: {{ .Values.image.pullPolicy }} | ||
| # delete all tmp files older than walltime limit | ||
| - name: galaxy-cron-{{ $key }} | ||
| {{- if $cronjob.image }} | ||
| image: {{ $cronjob.image.repository }}:{{ $cronjob.image.tag }} | ||
| {{- else }} | ||
| image: "{{ $.Values.image.repository }}:{{ $.Values.image.tag }}" | ||
| {{- end }} | ||
| imagePullPolicy: {{ $.Values.image.pullPolicy }} | ||
| {{- if or $cronjob.defaultEnv $cronjob.extraEnv }} | ||
| env: | ||
| {{- if $cronjob.defaultEnv }} | ||
| {{- include "galaxy.podEnvVars" $}} | ||
| {{- end }} | ||
| {{- if $cronjob.extraEnv }} | ||
| {{- range $env := $cronjob.extraEnv }} | ||
| - name: {{ $env.name }} | ||
| value: {{ tpl $env.value $ | quote }} | ||
| {{- end }} | ||
| {{- end }} | ||
| {{- end }} | ||
| command: | ||
| - find | ||
| - {{ .Values.persistence.mountPath }}/tmp | ||
| - '!' | ||
| - -newermt | ||
| - -{{ (index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800) }} seconds | ||
| - -type | ||
| - f | ||
| - -exec | ||
| - rm | ||
| - '{}' | ||
| - ; | ||
| {{- range $cmd := $cronjob.command }} | ||
| - {{ tpl $cmd $ | quote }} | ||
| {{- end}} | ||
| {{- if $cronjob.args }} | ||
| args: | ||
| {{- range $arg := $cronjob.args }} | ||
| - {{ tpl $arg $ | quote }} | ||
| {{- end }} | ||
| {{- end }} | ||
| volumeMounts: | ||
| - name: galaxy-data | ||
| mountPath: {{ .Values.persistence.mountPath }} | ||
| mountPath: {{ $.Values.persistence.mountPath }} | ||
| {{- range $key, $entry := $cronjob.extraFileMappings }} | ||
| - name: {{ include "galaxy.getExtraFilesUniqueName" $key }} | ||
| mountPath: {{ $key }} | ||
| subPath: {{ include "galaxy.getFilenameFromPath" $key }} | ||
| {{- end }} | ||
| volumes: | ||
| - name: galaxy-data | ||
| {{- if .Values.persistence.enabled }} | ||
| {{- if $.Values.persistence.enabled }} | ||
| persistentVolumeClaim: | ||
| claimName: {{ template "galaxy.pvcname" . }} | ||
| claimName: {{ template "galaxy.pvcname" $ }} | ||
| {{- else }} | ||
| emptyDir: {} | ||
| {{- end }} | ||
| {{- range $key, $entry := $cronjob.extraFileMappings }} | ||
| - name: {{ include "galaxy.getExtraFilesUniqueName" $key }} | ||
| {{- if $entry.useSecret }} | ||
| secret: | ||
| secretName: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $key) }} | ||
| {{- else }} | ||
| configMap: | ||
| name: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $key) }} | ||
| {{- end }} | ||
| {{- if $entry.mode }} | ||
| defaultMode: {{ $entry.mode }} | ||
| {{- end }} | ||
| {{- end }} | ||
| restartPolicy: OnFailure | ||
| {{- if $cronjob.extraFileMappings }} | ||
| {{- range $name, $entry := $cronjob.extraFileMappings }} | ||
| --- | ||
| apiVersion: v1 | ||
| metadata: | ||
| # Extract the filename portion only | ||
| name: {{ printf "%s-%s" (include "galaxy.fullname" $) (include "galaxy.getExtraFilesUniqueName" $name) }} | ||
| labels: | ||
| {{- include "galaxy.labels" $ | nindent 4 }} | ||
| {{- if $entry.useSecret }} | ||
| kind: Secret | ||
| type: Opaque | ||
| stringData: | ||
| {{- else }} | ||
| kind: ConfigMap | ||
| data: | ||
| {{- end }} | ||
| {{- include "galaxy.getFilenameFromPath" $name | nindent 2 }}: | | ||
| {{- if $entry.tpl }} | ||
| {{- tpl (tpl $entry.content $) $ | nindent 4 }} | ||
| {{- else }} | ||
| {{- $entry.content | nindent 4 }} | ||
| {{- end }} | ||
| {{- end }} | ||
| {{- end }} | ||
|
|
||
| {{- end }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| --- | ||
| apiVersion: apps/v1 | ||
| kind: Deployment | ||
| metadata: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| --- | ||
| apiVersion: apps/v1 | ||
| kind: Deployment | ||
| metadata: | ||
|
|
||
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