Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into add-pvs-to-molgenis
This commit is contained in:
sido
commit
88134dbccb
@ -104,7 +104,8 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
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- [Jenkins](molgenis-jenkins/README.md)
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- [Jenkins](molgenis-jenkins/README.md)
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- [NEXUS](molgenis-nexus/README.md)
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- [NEXUS](molgenis-nexus/README.md)
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- [HTTPD](molgenis-httpd/README.md)
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- [HTTPD](molgenis-httpd/README.md)
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- [MOLNIGES preview](molgenis-preview/README.md)
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- [MOLGENIS preview](molgenis-preview/README.md)
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- [MOLGENIS vault](molgenis-vault/README.md)
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### Useful commands
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### Useful commands
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You can you need to know to easily develop and deploy helm-charts
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You can you need to know to easily develop and deploy helm-charts
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21
molgenis-vault/.helmignore
Normal file
21
molgenis-vault/.helmignore
Normal file
@ -0,0 +1,21 @@
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# Patterns to ignore when building packages.
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# This supports shell glob matching, relative path matching, and
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# negation (prefixed with !). Only one pattern per line.
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.DS_Store
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# Common VCS dirs
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.git/
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.gitignore
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.bzr/
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.bzrignore
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.hg/
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.hgignore
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.svn/
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# Common backup files
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*.swp
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*.bak
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*.tmp
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*~
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# Various IDEs
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.project
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.idea/
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*.tmproj
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6
molgenis-vault/Chart.yaml
Normal file
6
molgenis-vault/Chart.yaml
Normal file
@ -0,0 +1,6 @@
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apiVersion: v1
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appVersion: "1.0"
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description: MOLGENIS vault
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name: molgenis-vault
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version: 0.1.1
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icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg
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52
molgenis-vault/README.md
Normal file
52
molgenis-vault/README.md
Normal file
@ -0,0 +1,52 @@
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# MOLGENIS Vault helm chart
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This chart creates a vault operator, but NO vault.
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The vault operator defines a new custom resource named `vault` that you can use to create vaults.
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After launching the operator, create the molgenis vault manually:
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`kubectl create -f resources/vault.yaml`
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That creates a new vault with two vault pods.
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See https://github.com/coreos/vault-operator/blob/master/doc/user/vault.md
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## Parameters
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### Azure cloud credentials
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Define credentials for backup to the Azure Blob Store.
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See [etcd-operator documentation](https://github.com/coreos/etcd-operator/blob/master/doc/user/abs_backup.md).
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| Parameter | Description | Default |
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| --------------- | ----------------------------- | ------------------ |
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| `abs.account` | name of storage account | `fdlkops` |
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| `abs.accessKey` | access key of storage account | `xxxx` |
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| `abs.cloud` | name of cloud environment | `AzurePublicCloud` |
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### Backup job
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Define the schedule of the backup job
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| Parameter | Description | Default |
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| -------------------- | ---------------------------- | ------------- |
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| `backupJob.enable` | Enable backup cronjob | `true` |
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| `backupJob.schedule` | cron schedule for the backup | `0 12 * * 1` |
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### UI
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Parameter | Description | Default
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--------- | ----------- | -------
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`ui.replicaCount` | desired number of Vault UI pod | `1`
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`ui.image.repository` | Vault UI container image repository | `djenriquez/vault-ui`
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`ui.image.tag` | Vault UI container image tag | `latest`
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`ui.resources` | Vault UI pod resource requests & limits | `{}`
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`ui.nodeSelector` | node labels for Vault UI pod assignment | `{}`
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`ui.ingress.enabled` | If true, Vault UI Ingress will be created | `true`
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`ui.ingress.annotations` | Vault UI Ingress annotations | `{}`
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`ui.ingress.host` | Vault UI Ingress hostname | `vault.molgenis.org`
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`ui.ingress.tls` | Vault UI Ingress TLS configuration (YAML) | `[]`
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`ui.vault.url` | Vault UI default vault url | `https://vault.vault-operator:8200`
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`ui.vault.auth` | Vault UI login method | `GITHUB`
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`ui.service.name` | Vault UI service name | `vault-ui`
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`ui.service.type` | type of ui service to create | `ClusterIP`
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`ui.service.externalPort` | Vault UI service target port | `8000`
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`ui.service.internalPort` | Vault UI container port | `8000`
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`ui.service.nodePort` | Port to be used as the service NodePort (ignored if `server.service.type` is not `NodePort`) | `0`
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627
molgenis-vault/catalogIcon-molgenis-vault.svg
Normal file
627
molgenis-vault/catalogIcon-molgenis-vault.svg
Normal file
@ -0,0 +1,627 @@
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k+t8EAfGbd26VaOOHDkiSWFhJ3jixInqd3vqqKjbVLjiUYjhEM1FHDgR3/g2CfEbNcRjqFcOV50Q
|
||||||
|
TgJw42LlypXKwP7+/ppMZD0PBJjBYBKPynLM1T/XFAsXLtQSPi6Enz9/rvGdnZ2Sr169kkR/Xns1
|
||||||
|
qc4H66Cfgrl69apGEyfiyJlOpTuuo6JhU+GKx/FEfHbnknhAaMOof+tk3KgjHoNxgMomc4dxdmu2
|
||||||
|
v39AseDq/tGjR7HY1PSjB72hSqefMz3vGc/ZyVVy0TOeBKgxfgTAD8aBud9w69YtjZ41a5YkhRWq
|
||||||
|
dPwlHiNUNfxauOJRiOHDRGf36odxIn4kA8Rr1BKP4aEz3Sufs+rw4cOKw/bt20fG4zfW88CQySSa
|
||||||
|
Yx8PnjFjhtZv9ozHjj///J/md3b+Lhk742ucqQOwK+THhg0bNOvUqVOSfobHcB2VDZsKVzwBSsRn
|
||||||
|
Z3zDKH/rHHPE4/Dw1u5bPZjHotljz3nz5mnqixcvWKJGxgLlle84dsb7me447xlPAdQYPwLgB+Mc
|
||||||
|
c3a/f/9es2KV7f0e9xGqG35tueJZ3Q34ESfi/47VmCE+71bPmc8Z9+DBA+VMV9cfkgMDWcZ75caw
|
||||||
|
BxI8ZcoUrXvjxg3JZcuWSaI/tC6Vef/+fY3nzh33HVhfnQ0+GBfSRzx4UaW7+z9araMj2xG9srkV
|
||||||
|
PGnSJI1z3MCUul0tV3wivm5c/6nsMUc8DpHZP27tta9iDfdnP+944Wvz5s2K3IkTJyRZN1SRzfbz
|
||||||
|
PH/37t1an4r2M53fy/yO379/v8bv3btXEnuYr8Y6H8SDcWC3u7u7W7MvXLggydNHr/QYHo5rdi1V
|
||||||
|
x6S6TYUrHkdwzA0I40T830yMWuLJ6DDBXM2HKj/rZ50tW7YoM48ePSpJO5XmiUY/iRfDvb29WvfA
|
||||||
|
gQOSoY+i78hhB3a63eBVq1ZJ9eXLlyU5s2OV7Wc649mh0B/yy9sLVzyBTsRnISXwY554HMThoglA
|
||||||
|
JXDVzNVtX1/2pg56GNcq5jVn3oXj6pprAJ4hoI8E94oB4z/jwG7nokWLNOX69euSM2fOlORag9/z
|
||||||
|
XtmOqXTGe9yxKyYLVzyO4agbkBcT4ER89mKFE+34lxNPhuclmMoKjedePgmwbds2JS3vl6OPRPt/
|
||||||
|
42jFfP9DEgqABHbMO3unT5/Wkjx1cwKL4lF7xpMIifjs5Um28LyJ8MuIpzIgMFbZ9PuNHzD9VM6m
|
||||||
|
TZuk4syZM5IDA9lz/VCFMa9oPzsJfrmM7TgkcE9Pj6aeO3dOEoJaPdM9ITzubm8IFz7jPUBuQAxD
|
||||||
|
NIECJ+KzP+TI+zPP4xwi2ttbJt4V/2yMwXfu3NHXNWvWSPKee6wC8/ajJyRZJ7Sj8Gzg0qVLWqKr
|
||||||
|
q0sydEfOL9oce2WD2Tm408jbt9gXst/bE/HfL9I8MI4JbCKem+3fIxSrdLZy39rBnsGOmU+Gcw/9
|
||||||
|
5MmTsoDn+jzXznvG+5EVIpxx2Ms7cpzlx44d01S3m0oNXbTlrXTmc41AHEhEjki3P4RbrngWTsT/
|
||||||
|
y4iPEd5sPxkcqljWo/I46588eaIcvHnzpiRP13g/noplyyZhQ5Jx/K1eb+9ODe3p+a/k4sWLJbkD
|
||||||
|
12xl56300JnuOwv2hvzx9pYrHiLYalrFifjsDh6JVFniySQnnDOZynTsGRvDnG0EYhhnb6wMDmZP
|
||||||
|
ATn7sAt57do1fb17964k1wQk2ty5c9XOPXV+PXC2sg52kuhgxkHYz8LDfk6QCWD8ZCdjh8TOmGy5
|
||||||
|
4lGQiK+t1DFPvBPeLKbiyNhmMRlPAiJpZ13aQ2ch/8lSW1v2ogiVzI4FZsdptrJ/1pmOPeyg2IN/
|
||||||
|
eWXLFd8s0T6+WaJ9PAS7w7Qn4j0yGW6ZeJYlAz0jwVQMZ1MMc5aR0SHMeujn7A0lmFe8JwiJxTqs
|
||||||
|
ix7sCG3lXtmOYzsF67vf6Mce4ur2wkdMJuK/34hiZ/BAEmgCDzH/euK9smKYwHqg82Iq1DOadioa
|
||||||
|
zLpuF4RSOWAnmMqLVWrRftYP7YDYh/34h//sTN5Of0i2XPEYhAExnIivvfoftcSTUVQMGRrKYCrK
|
||||||
|
+9lCCUQI+3z0ecKRYF4JvhMwjsTFD/RgR2hr90oveqajz+Pi2P10f+AjJluueBQQMIhwg2OYACfi
|
||||||
|
PyukoUT45cRDOBVDZZGBMczZy3ywz4/1Mx57ikrWKWq3EwLGL/cjhrGH+b4e/diLzOt/4YpHAQ6g
|
||||||
|
2A0KYRxiPtjHx/oZjz1FJevE/MBOtwtiODLAofE+3zH2MN/Xox97kXn9b5n4vIrSuGpFIBFfLT5K
|
||||||
|
syYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrMmEV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqz
|
||||||
|
JhFfWqirpSgRXy0+SrMmEV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrMm
|
||||||
|
EV9aqKulKBFfLT5KsyYRX1qoq6UoEV8tPkqzJhFfWqirpSgRXy0+SrPmL/hk6fsEzapeAAAAAElF
|
||||||
|
TkSuQmCC
|
||||||
|
"
|
||||||
|
style="image-rendering:optimizeQuality"
|
||||||
|
preserveAspectRatio="none"
|
||||||
|
height="94.666664"
|
||||||
|
width="84" /><g
|
||||||
|
inkscape:groupmode="layer"
|
||||||
|
id="layer1"
|
||||||
|
inkscape:label="base"
|
||||||
|
style="opacity:1" /></svg>
|
||||||
|
After Width: | Height: | Size: 46 KiB |
BIN
molgenis-vault/charts/etcd-operator-0.8.0.tgz
Normal file
BIN
molgenis-vault/charts/etcd-operator-0.8.0.tgz
Normal file
Binary file not shown.
BIN
molgenis-vault/charts/vault-operator-0.1.1.tgz
Normal file
BIN
molgenis-vault/charts/vault-operator-0.1.1.tgz
Normal file
Binary file not shown.
9
molgenis-vault/requirements.lock
Normal file
9
molgenis-vault/requirements.lock
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
dependencies:
|
||||||
|
- name: vault-operator
|
||||||
|
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||||
|
version: 0.1.1
|
||||||
|
- name: etcd-operator
|
||||||
|
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||||
|
version: 0.8.0
|
||||||
|
digest: sha256:47aa645df7dfce9760905800321599de05995ae50090735d45310936dbaa46de
|
||||||
|
generated: 2018-09-06T18:59:39.861922543+02:00
|
||||||
7
molgenis-vault/requirements.yaml
Normal file
7
molgenis-vault/requirements.yaml
Normal file
@ -0,0 +1,7 @@
|
|||||||
|
dependencies:
|
||||||
|
- name: vault-operator
|
||||||
|
version: ^0.1.1
|
||||||
|
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||||
|
- name: etcd-operator
|
||||||
|
version: ^0.8.0
|
||||||
|
repository: https://kubernetes-charts.storage.googleapis.com/
|
||||||
15
molgenis-vault/resources/restore.yaml
Normal file
15
molgenis-vault/resources/restore.yaml
Normal file
@ -0,0 +1,15 @@
|
|||||||
|
# Use kubectl create -f restore.yaml to manually execute a restore of the vault
|
||||||
|
apiVersion: "etcd.database.coreos.com/v1beta2"
|
||||||
|
kind: "EtcdRestore"
|
||||||
|
metadata:
|
||||||
|
# The restore CR name must be the same as spec.etcdCluster.name
|
||||||
|
name: vault-etcd
|
||||||
|
namespace: vault-operator
|
||||||
|
spec:
|
||||||
|
etcdCluster:
|
||||||
|
# The namespace is the same as this EtcdRestore CR
|
||||||
|
name: vault-etcd
|
||||||
|
backupStorageType: ABS
|
||||||
|
abs:
|
||||||
|
path: vault/backup-<specify the backup name>
|
||||||
|
absSecret: abs
|
||||||
9
molgenis-vault/resources/vault.yaml
Normal file
9
molgenis-vault/resources/vault.yaml
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
# Use kubectl create -f vault.yaml to manually create a vault
|
||||||
|
apiVersion: "vault.security.coreos.com/v1alpha1"
|
||||||
|
kind: "VaultService"
|
||||||
|
metadata:
|
||||||
|
name: "vault"
|
||||||
|
namespace: "vault-operator"
|
||||||
|
spec:
|
||||||
|
nodes: 2
|
||||||
|
version: "0.9.1-0"
|
||||||
13
molgenis-vault/templates/NOTES.txt
Normal file
13
molgenis-vault/templates/NOTES.txt
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
Vault operator created
|
||||||
|
|
||||||
|
Next steps:
|
||||||
|
|
||||||
|
* Manually create a vault using resources/vault.yaml
|
||||||
|
* Manually restore a backup using resources/backup.yaml
|
||||||
|
* Unseal the vault pods
|
||||||
|
|
||||||
|
{{ if .Values.backupJob.enable }}
|
||||||
|
!! Make sure to check if the backups succeed !!
|
||||||
|
{{ else }}
|
||||||
|
!!!!!! NO BACKUPS CONFIGURED !!!!!!
|
||||||
|
{{ end }}
|
||||||
54
molgenis-vault/templates/_helpers.tpl
Normal file
54
molgenis-vault/templates/_helpers.tpl
Normal file
@ -0,0 +1,54 @@
|
|||||||
|
{{/*
|
||||||
|
Define vault ui fullname
|
||||||
|
*/}}
|
||||||
|
{{- define "vault.ui.fullname" -}}
|
||||||
|
{{- printf "%s-ui" .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
|
|
||||||
|
{{/*
|
||||||
|
Define vault service url for the ui
|
||||||
|
*/}}
|
||||||
|
{{- define "vault.service.url" -}}
|
||||||
|
{{- printf "https://%s:8200" .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
|
|
||||||
|
{{/* See https://github.com/helm/helm/issues/4535 */}}
|
||||||
|
{{- define "call-nested" }}
|
||||||
|
{{- $dot := index . 0 }}
|
||||||
|
{{- $subchart := index . 1 }}
|
||||||
|
{{- $template := index . 2 }}
|
||||||
|
{{- include $template (dict "Chart" (dict "Name" $subchart) "Values" (index $dot.Values $subchart) "Release" $dot.Release "Capabilities" $dot.Capabilities) }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
{{/* vim: set filetype=mustache: */}}
|
||||||
|
{{/*
|
||||||
|
Expand the name of the chart.
|
||||||
|
*/}}
|
||||||
|
{{- define "molgenis-vault.name" -}}
|
||||||
|
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
|
|
||||||
|
{{/*
|
||||||
|
Create a default fully qualified app name.
|
||||||
|
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
||||||
|
If release name contains chart name it will be used as a full name.
|
||||||
|
*/}}
|
||||||
|
{{- define "molgenis-vault.fullname" -}}
|
||||||
|
{{- if .Values.fullnameOverride -}}
|
||||||
|
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- else -}}
|
||||||
|
{{- $name := default .Chart.Name .Values.nameOverride -}}
|
||||||
|
{{- if contains $name .Release.Name -}}
|
||||||
|
{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- else -}}
|
||||||
|
{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
|
{{- end -}}
|
||||||
|
{{- end -}}
|
||||||
|
|
||||||
|
{{/*
|
||||||
|
Create chart name and version as used by the chart label.
|
||||||
|
*/}}
|
||||||
|
{{- define "molgenis-vault.chart" -}}
|
||||||
|
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||||
|
{{- end -}}
|
||||||
10
molgenis-vault/templates/abs-secret.yaml
Normal file
10
molgenis-vault/templates/abs-secret.yaml
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
# Secret to access microsoft azure blob store
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: abs
|
||||||
|
type: Opaque
|
||||||
|
stringData:
|
||||||
|
storage-account: {{ .Values.abs.account }}
|
||||||
|
storage-key: {{ .Values.abs.accessKey }}
|
||||||
|
cloud: {{ .Values.abs.cloud }}
|
||||||
18
molgenis-vault/templates/backup-configmap.yaml
Normal file
18
molgenis-vault/templates/backup-configmap.yaml
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
# configmap to use as a template by the backup cronjob to create etcdbackup instances
|
||||||
|
apiVersion: v1
|
||||||
|
kind: ConfigMap
|
||||||
|
metadata:
|
||||||
|
name: backup-config
|
||||||
|
data:
|
||||||
|
backup_cr.yaml: |
|
||||||
|
apiVersion: "etcd.database.coreos.com/v1beta2"
|
||||||
|
kind: "EtcdBackup"
|
||||||
|
metadata:
|
||||||
|
generateName: vault-backup-
|
||||||
|
spec:
|
||||||
|
etcdEndpoints: ["https://vault-etcd-client:2379"]
|
||||||
|
storageType: ABS
|
||||||
|
clientTLSSecret: vault-etcd-client-tls
|
||||||
|
abs:
|
||||||
|
path: vault/backup.<NOW>
|
||||||
|
absSecret: abs
|
||||||
30
molgenis-vault/templates/backup-cronjob.yaml
Normal file
30
molgenis-vault/templates/backup-cronjob.yaml
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
{{- if .Values.backupJob.enable }}
|
||||||
|
# cronjob that creates etcdbackups using the etcd backup serviceaccount
|
||||||
|
apiVersion: batch/v1beta1
|
||||||
|
kind: CronJob
|
||||||
|
metadata:
|
||||||
|
name: etcd-backup
|
||||||
|
spec:
|
||||||
|
schedule: {{ .Values.backupJob.schedule | quote }}
|
||||||
|
jobTemplate:
|
||||||
|
spec:
|
||||||
|
template:
|
||||||
|
spec:
|
||||||
|
serviceAccountName: {{ include "call-nested" (list . "etcd-operator" "etcd-operator.serviceAccountName") }}
|
||||||
|
containers:
|
||||||
|
- name: etcd-backup
|
||||||
|
image: lachlanevenson/k8s-kubectl
|
||||||
|
command:
|
||||||
|
- /bin/sh
|
||||||
|
- "-ec"
|
||||||
|
- |
|
||||||
|
sed -e "s|<NOW>|$(date '+%Y-%m-%d_%H:%M:%S')|g" /var/etcd_backup/backup_cr.yaml | kubectl create -f -
|
||||||
|
volumeMounts:
|
||||||
|
- name: backup-config
|
||||||
|
mountPath: /var/etcd_backup
|
||||||
|
restartPolicy: OnFailure
|
||||||
|
volumes:
|
||||||
|
- name: backup-config
|
||||||
|
configMap:
|
||||||
|
name: backup-config
|
||||||
|
{{- end }}
|
||||||
30
molgenis-vault/templates/ui-ingress.yaml
Normal file
30
molgenis-vault/templates/ui-ingress.yaml
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
{{- if .Values.ui.ingress.enabled -}}
|
||||||
|
{{- $serviceName := include "vault.ui.fullname" . -}}
|
||||||
|
{{- $servicePort := .Values.ui.service.externalPort -}}
|
||||||
|
apiVersion: extensions/v1beta1
|
||||||
|
kind: Ingress
|
||||||
|
metadata:
|
||||||
|
name: {{ template "vault.ui.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis-vault.name" . }}
|
||||||
|
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
annotations:
|
||||||
|
{{- range $key, $value := .Values.ui.ingress.annotations }}
|
||||||
|
{{ $key }}: {{ $value | quote }}
|
||||||
|
{{- end }}
|
||||||
|
spec:
|
||||||
|
rules:
|
||||||
|
- host: {{ .Values.ui.ingress.host }}
|
||||||
|
http:
|
||||||
|
paths:
|
||||||
|
- path:
|
||||||
|
backend:
|
||||||
|
serviceName: {{ $serviceName }}
|
||||||
|
servicePort: {{ $servicePort }}
|
||||||
|
{{- if .Values.ui.ingress.tls }}
|
||||||
|
tls:
|
||||||
|
{{ toYaml .Values.ui.ingress.tls | indent 4 }}
|
||||||
|
{{- end -}}
|
||||||
|
{{- end -}}
|
||||||
23
molgenis-vault/templates/ui-service.yaml
Normal file
23
molgenis-vault/templates/ui-service.yaml
Normal file
@ -0,0 +1,23 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: Service
|
||||||
|
metadata:
|
||||||
|
name: {{ template "vault.ui.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "vault-operator.name" . }}
|
||||||
|
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
spec:
|
||||||
|
type: {{ .Values.ui.service.type }}
|
||||||
|
ports:
|
||||||
|
- port: {{ .Values.ui.service.externalPort }}
|
||||||
|
targetPort: {{ .Values.ui.service.internalPort }}
|
||||||
|
protocol: TCP
|
||||||
|
name: {{ .Values.ui.service.name }}
|
||||||
|
{{- if .Values.ui.service.nodePort }}
|
||||||
|
nodePort: {{ .Values.ui.service.nodePort }}
|
||||||
|
{{- end }}
|
||||||
|
selector:
|
||||||
|
app: {{ template "vault-operator.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
component: {{ .Values.ui.name }}
|
||||||
50
molgenis-vault/templates/vault-ui-deployment.yaml
Normal file
50
molgenis-vault/templates/vault-ui-deployment.yaml
Normal file
@ -0,0 +1,50 @@
|
|||||||
|
apiVersion: apps/v1beta1
|
||||||
|
kind: Deployment
|
||||||
|
metadata:
|
||||||
|
name: {{ template "vault.ui.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "vault-operator.name" . }}
|
||||||
|
chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
component: {{ .Values.ui.name }}
|
||||||
|
spec:
|
||||||
|
replicas: {{ .Values.ui.replicaCount }}
|
||||||
|
template:
|
||||||
|
metadata:
|
||||||
|
labels:
|
||||||
|
app: {{ template "vault-operator.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
component: {{ .Values.ui.name }}
|
||||||
|
spec:
|
||||||
|
containers:
|
||||||
|
- name: {{ .Values.ui.name }}
|
||||||
|
image: "{{ .Values.ui.image.repository }}:{{ .Values.ui.image.tag }}"
|
||||||
|
imagePullPolicy: {{ .Values.imagePullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: VAULT_URL_DEFAULT
|
||||||
|
{{- if .Values.ui.vault.url }}
|
||||||
|
value: {{ .Values.ui.vault.url }}
|
||||||
|
{{ else }}
|
||||||
|
value: {{ template "vault.service.url" . }}
|
||||||
|
{{- end }}
|
||||||
|
- name: VAULT_AUTH_DEFAULT
|
||||||
|
value: {{ .Values.ui.vault.auth }}
|
||||||
|
- name: NODE_TLS_REJECT_UNAUTHORIZED
|
||||||
|
value: '0'
|
||||||
|
ports:
|
||||||
|
- containerPort: {{ .Values.ui.service.internalPort }}
|
||||||
|
livenessProbe:
|
||||||
|
httpGet:
|
||||||
|
path: /
|
||||||
|
port: {{ .Values.ui.service.internalPort }}
|
||||||
|
readinessProbe:
|
||||||
|
httpGet:
|
||||||
|
path: /
|
||||||
|
port: {{ .Values.ui.service.internalPort }}
|
||||||
|
resources:
|
||||||
|
{{ toYaml .Values.ui.resources | indent 12 }}
|
||||||
|
{{- if .Values.ui.nodeSelector }}
|
||||||
|
nodeSelector:
|
||||||
|
{{ toYaml .Values.ui.nodeSelector | indent 8 }}
|
||||||
|
{{- end }}
|
||||||
79
molgenis-vault/values.yaml
Normal file
79
molgenis-vault/values.yaml
Normal file
@ -0,0 +1,79 @@
|
|||||||
|
# Default values for molgenis-vault.
|
||||||
|
# This is a YAML-formatted file.
|
||||||
|
# Declare variables to be passed into your templates.
|
||||||
|
|
||||||
|
# abs gives details of the credentials to reach the azure backup storage
|
||||||
|
abs:
|
||||||
|
# account is the name of the Storage account
|
||||||
|
account: fdlkops
|
||||||
|
# access key for the Storage account
|
||||||
|
accessKey: xxxx
|
||||||
|
# default cloud
|
||||||
|
cloud: AzurePublicCloud
|
||||||
|
|
||||||
|
# backupjob describes the backup cronjob
|
||||||
|
backupJob:
|
||||||
|
# enable enables the backup job
|
||||||
|
enable: true
|
||||||
|
# schedule gives the cron schedule for the backup job
|
||||||
|
schedule: "0 12 * * 1"
|
||||||
|
|
||||||
|
###
|
||||||
|
# All of the config variables related to setting up the etcd-operator
|
||||||
|
# If you want more information about the variables exposed, please visit:
|
||||||
|
# https://github.com/kubernetes/charts/tree/master/stable/etcd-operator#configuration
|
||||||
|
###
|
||||||
|
etcd-operator:
|
||||||
|
deployments:
|
||||||
|
etcdOperator: true
|
||||||
|
backupOperator: true
|
||||||
|
restoreOperator: true
|
||||||
|
serviceAccount:
|
||||||
|
etcdOperatorServiceAccount:
|
||||||
|
create: true
|
||||||
|
backupOperatorServiceAccount:
|
||||||
|
create: true
|
||||||
|
restoreOperatorServiceAccount:
|
||||||
|
create: true
|
||||||
|
etcdOperator:
|
||||||
|
image:
|
||||||
|
tag: v0.9.2
|
||||||
|
backupOperator:
|
||||||
|
image:
|
||||||
|
tag: v0.9.2
|
||||||
|
restoreOperator:
|
||||||
|
image:
|
||||||
|
tag: v0.9.2
|
||||||
|
|
||||||
|
ui:
|
||||||
|
name: "vault-ui"
|
||||||
|
replicaCount: 1
|
||||||
|
image:
|
||||||
|
repository: djenriquez/vault-ui
|
||||||
|
tag: latest
|
||||||
|
service:
|
||||||
|
name: vault-ui
|
||||||
|
type: ClusterIP
|
||||||
|
externalPort: 8000
|
||||||
|
internalPort: 8000
|
||||||
|
# nodePort: 32001
|
||||||
|
ingress:
|
||||||
|
enabled: true
|
||||||
|
# Used to create Ingress record (should used with service.type: ClusterIP).
|
||||||
|
host: vault.molgenis.org
|
||||||
|
|
||||||
|
resources: {}
|
||||||
|
# We usually recommend not to specify default resources and to leave this as a conscious
|
||||||
|
# choice for the user. This also increases chances charts run on environments with little
|
||||||
|
# resources, such as Minikube. If you do want to specify resources, uncomment the following
|
||||||
|
# lines, adjust them as necessary, and remove the curly braces after 'resources:'.
|
||||||
|
# limits:
|
||||||
|
# cpu: 100m
|
||||||
|
# memory: 128Mi
|
||||||
|
#requests:
|
||||||
|
# cpu: 100m
|
||||||
|
# memory: 128Mi
|
||||||
|
nodeSelector: {}
|
||||||
|
vault:
|
||||||
|
auth: GITHUB
|
||||||
|
url: https://vault.vault-operator:8200
|
||||||
@ -2,7 +2,7 @@ apiVersion: v1
|
|||||||
appVersion: "1.0"
|
appVersion: "1.0"
|
||||||
description: MOLGENIS - helm stack (in BETA)
|
description: MOLGENIS - helm stack (in BETA)
|
||||||
name: molgenis-beta
|
name: molgenis-beta
|
||||||
version: 0.0.1
|
version: 0.1.0
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
||||||
@ -6,8 +6,8 @@ This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
|
|||||||
|
|
||||||
- MOLGENIS
|
- MOLGENIS
|
||||||
|
|
||||||
## Versions
|
## Provisioning
|
||||||
You can choose from which registry you want to pull from. There are 2:
|
You can choose from which registry you want to pull. There are 2 registries:
|
||||||
- https://registry.molgenis.org
|
- https://registry.molgenis.org
|
||||||
- https://hub.docker.com
|
- https://hub.docker.com
|
||||||
|
|
||||||
@ -18,6 +18,9 @@ The three properties you need to specify are:
|
|||||||
- ```molgenis.image.name```
|
- ```molgenis.image.name```
|
||||||
- ```molgenis.image.tag```
|
- ```molgenis.image.tag```
|
||||||
|
|
||||||
|
Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property.
|
||||||
|
- ```molgenis.adminPassword```
|
||||||
|
|
||||||
## Services
|
## Services
|
||||||
When you start MOLGENIS you need:
|
When you start MOLGENIS you need:
|
||||||
- an elasticsearch instance (5.5.6)
|
- an elasticsearch instance (5.5.6)
|
||||||
@ -64,19 +67,15 @@ You can specify the location of the OpenCPU cluster by specifying this property:
|
|||||||
You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
|
You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
|
||||||
|
|
||||||
## Resources
|
## Resources
|
||||||
You can specify resources by resource type. There are 3 resource types.
|
You can specify resources by resource type. There are 2 resource types.
|
||||||
- cpu's
|
|
||||||
- memory of container
|
- memory of container
|
||||||
- memory of JVM
|
- maximum heap space JVM
|
||||||
|
|
||||||
Specify number of cpu's:
|
|
||||||
- ```molgenis.resources.limits.cpu```
|
|
||||||
|
|
||||||
Specify memory usage of container:
|
Specify memory usage of container:
|
||||||
- ```molgenis.resources.limits.memory```
|
- ```molgenis.resources.limits.memory```
|
||||||
|
|
||||||
Specify memory usage for Java JVM:
|
Specify memory usage for Java JVM:
|
||||||
- ```molgenis.javaOpts```
|
- ```molgenis.javaOpts.maxHeapSpace```
|
||||||
|
|
||||||
Select the resources you need dependant on the customer you need to serve.
|
Select the resources you need dependant on the customer you need to serve.
|
||||||
|
|
||||||
|
|||||||
@ -3,13 +3,14 @@ categories:
|
|||||||
- MOLGENIS
|
- MOLGENIS
|
||||||
questions:
|
questions:
|
||||||
- variable: ingress.hosts[0].name
|
- variable: ingress.hosts[0].name
|
||||||
|
label: Hostname
|
||||||
default: "test.molgenis.org"
|
default: "test.molgenis.org"
|
||||||
description: "Hostname for your stack"
|
description: "Hostname for your stack"
|
||||||
type: hostname
|
type: hostname
|
||||||
required: true
|
required: true
|
||||||
group: "Load Balancing"
|
group: "Load Balancing"
|
||||||
label: Hostname
|
|
||||||
- variable: molgenis.image.repository
|
- variable: molgenis.image.repository
|
||||||
|
label: Registry
|
||||||
default: "registry.hub.docker.com"
|
default: "registry.hub.docker.com"
|
||||||
description: "Select a registry to pull from"
|
description: "Select a registry to pull from"
|
||||||
type: enum
|
type: enum
|
||||||
@ -17,95 +18,82 @@ questions:
|
|||||||
- "registry.hub.docker.com"
|
- "registry.hub.docker.com"
|
||||||
- "registry.molgenis.org"
|
- "registry.molgenis.org"
|
||||||
required: true
|
required: true
|
||||||
group: "Version"
|
group: "Provisioning"
|
||||||
label: Registry
|
|
||||||
- variable: molgenis.image.tag
|
- variable: molgenis.image.tag
|
||||||
default: "stable"
|
label: Version
|
||||||
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
|
default: ""
|
||||||
|
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Version"
|
group: "Provisioning"
|
||||||
label: Version
|
- variable: molgenis.adminPassword
|
||||||
|
label: Administrator password
|
||||||
|
default: ""
|
||||||
|
description: "Enter an administrator password"
|
||||||
|
type: password
|
||||||
|
required: true
|
||||||
|
group: "Provisioning"
|
||||||
- variable: molgenis.services.opencpu.host
|
- variable: molgenis.services.opencpu.host
|
||||||
|
label: OpenCPU cluster
|
||||||
default: "localhost"
|
default: "localhost"
|
||||||
description: "Specify the OpenCPU cluster"
|
description: "Specify the OpenCPU cluster"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
label: OpenCPU cluster
|
|
||||||
- variable: molgenis.services.postgres.host
|
- variable: molgenis.services.postgres.host
|
||||||
|
label: Postgres cluster location
|
||||||
default: "postgresql.molgenis-postgresql.svc"
|
default: "postgresql.molgenis-postgresql.svc"
|
||||||
description: "Set the location of the postgres cluster"
|
description: "Set the location of the postgres cluster"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
label: Postgres cluster location
|
|
||||||
- variable: molgenis.services.postgres.scheme
|
- variable: molgenis.services.postgres.scheme
|
||||||
|
label: Database scheme
|
||||||
default: "molgenis"
|
default: "molgenis"
|
||||||
description: "Set the database scheme"
|
description: "Set the database scheme"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
label: Database scheme
|
|
||||||
- variable: molgenis.services.postgres.user
|
- variable: molgenis.services.postgres.user
|
||||||
|
label: Database username
|
||||||
default: "molgenis"
|
default: "molgenis"
|
||||||
description: "Set user of the database scheme"
|
description: "Set user of the database scheme"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
label: Database username
|
|
||||||
- variable: molgenis.services.postgres.password
|
- variable: molgenis.services.postgres.password
|
||||||
|
label: Database password
|
||||||
default: "molgenis"
|
default: "molgenis"
|
||||||
description: "Set the password of the database scheme"
|
description: "Set the password of the database scheme"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
label: Database password
|
|
||||||
- variable: molgenis.resources.limits.cpu
|
|
||||||
default: 1
|
|
||||||
description: "CPU limit for this MOLGENIS instance"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "1"
|
|
||||||
- "2"
|
|
||||||
- "3"
|
|
||||||
- "4"
|
|
||||||
required: true
|
|
||||||
group: "Resources"
|
|
||||||
label: CPU limit
|
|
||||||
- variable: molgenis.resources.limits.memory
|
- variable: molgenis.resources.limits.memory
|
||||||
|
label: Container memory limit
|
||||||
default: 1250Mi
|
default: 1250Mi
|
||||||
description: "Memory limit for this MOLGENIS instance"
|
description: "Memory limit for this MOLGENIS container"
|
||||||
type: enum
|
type: enum
|
||||||
options:
|
options:
|
||||||
- "1250Mi"
|
- "1250Mi"
|
||||||
- "1500Mi"
|
|
||||||
- "2000Mi"
|
|
||||||
- "2500Mi"
|
- "2500Mi"
|
||||||
required: true
|
required: true
|
||||||
group: "Resources"
|
group: "Resources"
|
||||||
label: Memory limit
|
- variable: molgenis.resources.requests.memory
|
||||||
- variable: molgenis.javaOpts
|
label: Container memory reservation
|
||||||
default: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
default: 1250Mi
|
||||||
description: "Java runtime options for the MOLGENIS instance"
|
description: "Memory reservation for this MOLGENIS container"
|
||||||
type: enum
|
type: enum
|
||||||
options:
|
options:
|
||||||
- "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
- "1250Mi"
|
||||||
- "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
- "2500Mi"
|
||||||
group: "Resources"
|
|
||||||
label: Java memory options
|
|
||||||
- variable: molgenis.persistence.enabled
|
|
||||||
default: false
|
|
||||||
description: "Do you want to use persistance"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
required: true
|
||||||
group: "Persistence"
|
group: "Resources"
|
||||||
label: Persistence
|
- variable: molgenis.javaOpts.maxHeapSpace
|
||||||
show_subquestion_if: true
|
label: Maximum heap space (JVM)
|
||||||
subquestions:
|
default: "1g"
|
||||||
- variable: molgenis.persistence.size
|
description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit"
|
||||||
default: "30Gi"
|
type: enum
|
||||||
description: "Size of MOLGENIS filestore (not the database size)"
|
options:
|
||||||
type: string
|
- "1g"
|
||||||
label: Size filestore
|
- "2g"
|
||||||
|
group: "Resources"
|
||||||
@ -46,7 +46,7 @@ spec:
|
|||||||
- name: admin.password
|
- name: admin.password
|
||||||
value: {{ .adminPassword }}
|
value: {{ .adminPassword }}
|
||||||
- name: CATALINA_OPTS
|
- name: CATALINA_OPTS
|
||||||
value: {{ .javaOpts }}
|
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||||
ports:
|
ports:
|
||||||
- containerPort: 8080
|
- containerPort: 8080
|
||||||
{{- if .persistence.enabled }}
|
{{- if .persistence.enabled }}
|
||||||
@ -58,14 +58,18 @@ spec:
|
|||||||
httpGet:
|
httpGet:
|
||||||
path: /
|
path: /
|
||||||
port: 8080
|
port: 8080
|
||||||
initialDelaySeconds: 180
|
initialDelaySeconds: 60
|
||||||
periodSeconds: 5
|
periodSeconds: 5
|
||||||
|
failureThreshold: 25
|
||||||
|
successThreshold: 1
|
||||||
readinessProbe:
|
readinessProbe:
|
||||||
httpGet:
|
httpGet:
|
||||||
path: /api/v2/version
|
path: /api/v2/version
|
||||||
port: 8080
|
port: 8080
|
||||||
initialDelaySeconds: 180
|
initialDelaySeconds: 120
|
||||||
periodSeconds: 5
|
periodSeconds: 30
|
||||||
|
failureThreshold: 3
|
||||||
|
successThreshold: 1
|
||||||
resources:
|
resources:
|
||||||
{{ toYaml .resources | indent 12 }}
|
{{ toYaml .resources | indent 12 }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
|
|||||||
@ -17,19 +17,20 @@ ingress:
|
|||||||
|
|
||||||
molgenis:
|
molgenis:
|
||||||
image:
|
image:
|
||||||
repository: registry.molgenis.org
|
repository: registry.hub.docker.com
|
||||||
name: molgenis/molgenis-app
|
name: molgenis/molgenis-app
|
||||||
tag: stable
|
tag: stable
|
||||||
pullPolicy: Always
|
pullPolicy: Always
|
||||||
adminPassword: admin
|
adminPassword:
|
||||||
javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
javaOpts:
|
||||||
|
maxHeapSpace: "1g"
|
||||||
resources:
|
resources:
|
||||||
limits:
|
limits:
|
||||||
cpu: 1
|
cpu: 1
|
||||||
memory: 1250Mi
|
memory: 1250Mi
|
||||||
requests:
|
requests:
|
||||||
cpu: 200m
|
cpu: 200m
|
||||||
memory: 1Gi
|
memory: 1250Mi
|
||||||
persistence:
|
persistence:
|
||||||
enabled: false
|
enabled: false
|
||||||
name: molgenis-nfs-claim
|
name: molgenis-nfs-claim
|
||||||
@ -51,12 +52,12 @@ elasticsearch:
|
|||||||
repository: docker.elastic.co/elasticsearch/elasticsearch
|
repository: docker.elastic.co/elasticsearch/elasticsearch
|
||||||
tag: 5.5.3
|
tag: 5.5.3
|
||||||
pullPolicy: IfNotPresent
|
pullPolicy: IfNotPresent
|
||||||
javaOpts: "-Xms512m -Xmx512m"
|
javaOpts: "-Xms1g -Xmx1g"
|
||||||
clusterName: molgenis
|
clusterName: molgenis
|
||||||
resources:
|
resources:
|
||||||
limits:
|
limits:
|
||||||
cpu: 1
|
cpu: 2
|
||||||
memory: 1500Mi
|
memory: 3Gi
|
||||||
requests:
|
requests:
|
||||||
cpu: 100m
|
cpu: 100m
|
||||||
memory: 1Gi
|
memory: 1Gi
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user