Compare commits
2 Commits
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...
54aa4dff9e
| Author | SHA1 | Date |
|---|---|---|
Fleur Kelpin
|
54aa4dff9e | |
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Fleur Kelpin
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33d8a30c69 |
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@ -0,0 +1,16 @@
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apiVersion: v1
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entries:
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molgenis-preview:
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- apiVersion: v1
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||||||
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appVersion: "1.0"
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created: 2018-09-11T16:11:49.165533266+02:00
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description: MOLGENIS - helm stack for testing purposes
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digest: e1174bd0d8a71bf4d23f5463521cf4dbcac39dc93f16cd842c92cda1a963f6b2
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icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
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name: molgenis-preview
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sources:
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- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
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urls:
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- molgenis-preview-0.2.0.tgz
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version: 0.2.0
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generated: 2018-09-11T16:11:49.158086031+02:00
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Binary file not shown.
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@ -40,62 +40,57 @@ You can use [all configuration values of the jenkins subchart](https://github.co
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### GitHub Authentication delegation
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### GitHub Authentication delegation
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||||||
You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
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You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
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### Secrets
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### Additional configuration
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There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
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When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
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* PipelineSecrets
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|
|
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When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins
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build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
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each other with their own secrets.
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You can override the values at deploy time but otherwise also configure them
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You can override the values at deploy time but otherwise also configure them
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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#### Vault
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* Vault
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The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
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New vault token to be used by the pods to retrieve their tokens from the vault.
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|
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| Parameter | Description | Default |
|
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| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
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| `secret.vault.token` | Token to log into the hashicorp vault | `xxxx` |
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| `secret.vault.addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
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| `secret.vault.skipVerify` | Skip verification of the https connection | `1` |
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#### GitHub
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|
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Token used by Jenkins to authenticate on GitHub.
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| Parameter | Description | Default |
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| --------------------- | ------------------------ | ------------------ |
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| `secret.gitHub.user` | username for the account | `molgenis-jenkins` |
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| `secret.gitHub.token` | token for the account | `xxxx` |
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#### Gogs
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|
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Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
|
|
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| Parameter | Description | Default |
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|
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| ------------------- | ------------------------ | --------- |
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| `secret.gogs.user` | username for the account | `p281392` |
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| `secret.gogs.token` | token for the account | `xxxx` |
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#### Legacy:
|
|
||||||
|
|
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##### Docker Hub
|
|
||||||
|
|
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Account used in pipeline builds to push docker images to `hub.docker.com`.
|
| Parameter | Description | Default |
|
||||||
> They should read `secret/gcc/account/dockerhub` from vault instead!
|
| ---------------------------------- | ------------------------------------------ | ---------------------------------------------- |
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| `PipelineSecrets.Vault.Replace` | Replace the molgenis-pipeline-vault secret | `true` |
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| `PipelineSecrets.Vault.Token` | Token to log into the hashicorp vault | `xxxx` |
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| `PipelineSecrets.Vault.Addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
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| `PipelineSecrets.Vault.SkipVerify` | Skip verification of the https connection | `1` |
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|
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| Parameter | Description | Default |
|
* Env
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| --------------------------- | ------------------------ | --------------- |
|
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| `secret.dockerHub.user` | username for the account | `molgenisci` |
|
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| `secret.dockerHub.password` | password for the account | `xxxx` |
|
|
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|
|
||||||
##### Registry
|
|
||||||
|
|
||||||
Account used in pipeline builds to push docker images to `registry.molgenis.org`.
|
Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
|
||||||
> They should read `secret/ops/account/nexus` from vault instead!
|
in the slave pods.
|
||||||
|
|
||||||
| Parameter | Description | Default |
|
| Parameter | Description | Default |
|
||||||
| --------------------------- | ------------------------ | --------- |
|
| --------------------------------------- | ----------------------------------------- | --------------- |
|
||||||
| `secret.dockerHub.user` | username for the account | `admin` |
|
| `PipelineSecrets.Env.Replace` | Replace molgenis-pipeline-env secret | `true` |
|
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| `secret.dockerHub.password` | password for the account | `xxxx` |
|
| `PipelineSecrets.Env.PGPPassphrase` | passphrase for the pgp signing key | `literal:xxxx` |
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| `PipelineSecrets.Env.CodecovToken` | token for codecov.io | `xxxx` |
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| `PipelineSecrets.Env.GitHubToken` | token for GH molgenis-jenkins user | `xxxx` |
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| `PipelineSecrets.Env.NexusPassword` | token for molgenis-jenkins user in NEXUS | `xxxx` |
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| `PipelineSecrets.Env.DockerHubPassword` | token for molgenis user in hub.docker.com | `xxxx` |
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| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` |
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| `PipelineSecrets.Env.NpmToken` | token for npmjs.org | `xxxx` |
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| `PipelineSecrets.Env.SauceAccessKey` | token for saucelabs.com | `xxxx` |
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* File
|
||||||
|
|
||||||
|
Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
|
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|
in the `/root/.m2` directory of the slave pods.
|
||||||
|
> The settings.xml file references the
|
||||||
|
|
||||||
|
| Parameter | Description | Default |
|
||||||
|
| -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
|
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| `PipelineSecrets.File.Replace` | Replace molgenis-pipeline-file secret | `true` |
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| `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
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| `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml)) |
|
||||||
|
|
||||||
## Command line use
|
## Command line use
|
||||||
Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
|
Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
|
||||||
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|
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@ -8,9 +8,9 @@ metadata:
|
||||||
"jenkins.io/credentials-type": "usernamePassword"
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"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
|
annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
|
"jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
|
||||||
}
|
}
|
||||||
type: Opaque
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type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
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username: {{ "molgenisci" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
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password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
|
||||||
|
|
@ -8,9 +8,9 @@ metadata:
|
||||||
"jenkins.io/credentials-type": "usernamePassword"
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"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
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annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
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# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
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"jenkins.io/credentials-description" : "oauth token for the molgenis-jenkins github user"
|
||||||
}
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}
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type: Opaque
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type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.gitHub.user | b64enc | quote }}
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username: {{ "molgenis-jenkins" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.gitHub.token | b64enc | quote }}
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password: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
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||||||
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@ -8,9 +8,9 @@ metadata:
|
||||||
"jenkins.io/credentials-type": "usernamePassword"
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"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
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annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
|
"jenkins.io/credentials-description" : "user to authenticate against GOGS (git.webhosting.rug.nl)"
|
||||||
}
|
}
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.gogs.user | b64enc | quote }}
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username: {{ "p281392" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.gogs.token | b64enc | quote }}
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password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
|
||||||
|
|
@ -0,0 +1,16 @@
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
# this is the jenkins id.
|
||||||
|
name: "molgenis-jenkins-nexus-secret"
|
||||||
|
labels:
|
||||||
|
# so we know what type it is.
|
||||||
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
|
annotations: {
|
||||||
|
# description - can not be a label as spaces are not allowed
|
||||||
|
"jenkins.io/credentials-description" : "user to authenticate against NEXUS"
|
||||||
|
}
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
username: {{ "admin" | b64enc | quote }}
|
||||||
|
password: {{ .Values.PipelineSecrets.Env.NexusPassword | b64enc | quote }}
|
||||||
|
|
@ -1,17 +0,0 @@
|
||||||
apiVersion: v1
|
|
||||||
kind: Secret
|
|
||||||
metadata:
|
|
||||||
name: molgenis-jenkins-registry-secret
|
|
||||||
labels:
|
|
||||||
app: {{ template "jenkins.fullname" . }}
|
|
||||||
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
|
||||||
release: "{{ .Release.Name }}"
|
|
||||||
heritage: "{{ .Release.Service }}"
|
|
||||||
annotations: {
|
|
||||||
# description - can not be a label as spaces are not allowed
|
|
||||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
|
|
||||||
}
|
|
||||||
type: Opaque
|
|
||||||
data:
|
|
||||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
|
||||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
|
|
||||||
|
|
@ -0,0 +1,16 @@
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
# this is the jenkins id.
|
||||||
|
name: "molgenis-jenkins-saucelabs-secret"
|
||||||
|
labels:
|
||||||
|
# so we know what type it is.
|
||||||
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
|
annotations: {
|
||||||
|
# description - can not be a label as spaces are not allowed
|
||||||
|
"jenkins.io/credentials-description" : "user to authenticate against Saucelabs (saucelabs.com)"
|
||||||
|
}
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
username: {{ "molgenis-jenkins" | b64enc | quote }}
|
||||||
|
password: {{ .Values.PipelineSecrets.Env.SauceAccessKey | b64enc | quote }}
|
||||||
|
|
@ -0,0 +1,18 @@
|
||||||
|
{{- if .Values.PipelineSecrets.Env.Replace }}
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: molgenis-pipeline-env-secret
|
||||||
|
labels:
|
||||||
|
app: {{ template "jenkins.fullname" . }}
|
||||||
|
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||||
|
release: "{{ .Release.Name }}"
|
||||||
|
heritage: "{{ .Release.Service }}"
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
|
||||||
|
codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
|
||||||
|
githubToken: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
|
||||||
|
sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
|
||||||
|
npmToken: {{ .Values.PipelineSecrets.Env.NpmToken | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
|
|
@ -0,0 +1,15 @@
|
||||||
|
{{- if .Values.PipelineSecrets.File.Replace }}
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: molgenis-pipeline-file-secret
|
||||||
|
labels:
|
||||||
|
app: {{ template "jenkins.fullname" . }}
|
||||||
|
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||||
|
release: "{{ .Release.Name }}"
|
||||||
|
heritage: "{{ .Release.Service }}"
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
|
||||||
|
settings.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
|
|
@ -1,3 +1,4 @@
|
||||||
|
{{- if .Values.PipelineSecrets.Vault.Replace }}
|
||||||
apiVersion: v1
|
apiVersion: v1
|
||||||
kind: Secret
|
kind: Secret
|
||||||
metadata:
|
metadata:
|
||||||
|
|
@ -9,6 +10,7 @@ metadata:
|
||||||
heritage: "{{ .Release.Service }}"
|
heritage: "{{ .Release.Service }}"
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
token: {{ .Values.secret.vault.token | b64enc | quote }}
|
token: {{ .Values.PipelineSecrets.Vault.Token | b64enc | quote }}
|
||||||
addr: {{ .Values.secret.vault.addr | b64enc | quote }}
|
addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
|
||||||
skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}
|
skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
|
|
@ -368,8 +368,8 @@ jenkins:
|
||||||
install: true
|
install: true
|
||||||
Pods:
|
Pods:
|
||||||
molgenis:
|
molgenis:
|
||||||
Label: molgenis
|
Label: molgenisv2
|
||||||
NodeUsageMode: NORMAL
|
NodeUsageMode: EXCLUSIVE
|
||||||
volumes:
|
volumes:
|
||||||
- type: HostPath
|
- type: HostPath
|
||||||
hostPath: "/var/run/docker.sock"
|
hostPath: "/var/run/docker.sock"
|
||||||
|
|
@ -417,6 +417,39 @@ jenkins:
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-vault-secret
|
||||||
secretKey: addr
|
secretKey: addr
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
|
molgenis-legacy:
|
||||||
|
InheritFrom: molgenis
|
||||||
|
Label: molgenis
|
||||||
|
NodeUsageMode: NORMAL
|
||||||
|
volumes:
|
||||||
|
- type: Secret
|
||||||
|
secretName: molgenis-pipeline-file-secret
|
||||||
|
mountPath: "/home/jenkins/.m2"
|
||||||
|
Containers:
|
||||||
|
EnvVars:
|
||||||
|
- type: Secret
|
||||||
|
key: PGP_PASSPHRASE
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: pgpPassphrase
|
||||||
|
- type: KeyValue
|
||||||
|
key: PGP_SECRETKEY
|
||||||
|
value: "keyfile:/home.jenkins/.m2/key.asc"
|
||||||
|
- type: KeyValue
|
||||||
|
key: npm_config_registry
|
||||||
|
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
|
||||||
|
- type: Secret
|
||||||
|
key: SONAR_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: sonarToken
|
||||||
|
- type: Secret
|
||||||
|
key: CODECOV_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: codecovToken
|
||||||
|
- type: Secret
|
||||||
|
key: GITHUB_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: githubToken
|
||||||
|
NodeSelector: {}
|
||||||
node:
|
node:
|
||||||
Label: node-carbon
|
Label: node-carbon
|
||||||
NodeUsageMode: EXCLUSIVE
|
NodeUsageMode: EXCLUSIVE
|
||||||
|
|
@ -428,45 +461,155 @@ jenkins:
|
||||||
Command: cat
|
Command: cat
|
||||||
WorkingDir: /home/jenkins
|
WorkingDir: /home/jenkins
|
||||||
TTY: true
|
TTY: true
|
||||||
vault:
|
EnvVars:
|
||||||
Image: "vault"
|
- type: KeyValue
|
||||||
Command: cat
|
key: npm_config_registry
|
||||||
WorkingDir: /home/jenkins
|
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
|
||||||
TTY: true
|
- type: Secret
|
||||||
EnvVars:
|
key: CODECOV_TOKEN
|
||||||
- type: Secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
key: VAULT_TOKEN
|
secretKey: codecovToken
|
||||||
secretName: molgenis-pipeline-vault-secret
|
- type: Secret
|
||||||
secretKey: token
|
key: GITHUB_TOKEN
|
||||||
- type: Secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
key: VAULT_SKIP_VERIFY
|
secretKey: githubToken
|
||||||
secretName: molgenis-pipeline-vault-secret
|
- type: Secret
|
||||||
secretKey: skipVerify
|
key: NPM_TOKEN
|
||||||
- type: Secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
key: VAULT_ADDR
|
secretKey: npmToken
|
||||||
secretName: molgenis-pipeline-vault-secret
|
|
||||||
secretKey: addr
|
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
#secret contains configuration for the kubernetes secrets that jenkins can access
|
molgenis-it:
|
||||||
secret:
|
InheritFrom: molgenis
|
||||||
# vault configures the vault secret
|
Label: molgenis-it
|
||||||
vault:
|
NodeUsageMode: EXCLUSIVE
|
||||||
token: xxxx
|
Containers:
|
||||||
addr: "https://vault-operator.vault-operator.svc:8200"
|
elasticsearch:
|
||||||
skipVerify: "1"
|
Image: docker.elastic.co/elasticsearch/elasticsearch
|
||||||
# githubToken contains access token for jenkins bot account on github.com
|
ImageTag: 5.5.3
|
||||||
gitHub:
|
resources:
|
||||||
user: "molgenis-jenkins"
|
requests:
|
||||||
token: xxxx
|
cpu: "100m"
|
||||||
# gogs contains access token for jenkins bot account on RuG GoGs
|
memory: "1Gi"
|
||||||
gogs:
|
limits:
|
||||||
user: p281392
|
cpu: "1"
|
||||||
token: xxxx
|
memory: "1500Mi"
|
||||||
# registry contains credentials for registry.molgenis.org
|
EnvVars:
|
||||||
registry:
|
- type: KeyValue
|
||||||
user: admin
|
key: ES_JAVA_OPTS
|
||||||
password: xxxx
|
value: "-Xms512m -Xmx512m"
|
||||||
# dockerHubPassword contains password for hub.docker.com
|
- type: KeyValue
|
||||||
dockerHub:
|
key: cluster.name
|
||||||
user: molgenisci
|
value: molgenis
|
||||||
password: xxxx
|
- type: KeyValue
|
||||||
|
key: bootstrap.memory_lock
|
||||||
|
value: "true"
|
||||||
|
- type: KeyValue
|
||||||
|
key: xpack.security.enabled
|
||||||
|
value: "false"
|
||||||
|
- type: KeyValue
|
||||||
|
key: discovery.type
|
||||||
|
value: single-node
|
||||||
|
postgres:
|
||||||
|
Image: postgres
|
||||||
|
ImageTag: 9.6-alpine
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
cpu: "100m"
|
||||||
|
memory: "250Mi"
|
||||||
|
limits:
|
||||||
|
cpu: "1"
|
||||||
|
memory: "250Mi"
|
||||||
|
EnvVars:
|
||||||
|
- type: KeyValue
|
||||||
|
key: POSTGRES_USER
|
||||||
|
value: molgenis
|
||||||
|
- type: KeyValue
|
||||||
|
key: POSTGRES_PASSWORD
|
||||||
|
value: molgenis
|
||||||
|
- type: KeyValue
|
||||||
|
key: POSTGRES_DB
|
||||||
|
value: molgenis
|
||||||
|
opencpu:
|
||||||
|
Image: molgenis/opencpu
|
||||||
|
AlwaysPullImage: true
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
cpu: "100m"
|
||||||
|
memory: "256Mi"
|
||||||
|
limits:
|
||||||
|
cpu: "1"
|
||||||
|
memory: "512Mi"
|
||||||
|
NodeSelector: {}
|
||||||
|
PipelineSecrets:
|
||||||
|
Vault:
|
||||||
|
Replace: true
|
||||||
|
Token: xxxx
|
||||||
|
Addr: "https://vault-operator.vault-operator.svc:8200"
|
||||||
|
SkipVerify: 1
|
||||||
|
Env:
|
||||||
|
# Set to false to keep existing secret
|
||||||
|
Replace: true
|
||||||
|
# Passphrase for the pgp private key file, prefixed with literal:
|
||||||
|
PGPPassphrase: literal:xxxx
|
||||||
|
# Token for codecov.io service
|
||||||
|
CodecovToken: xxxx
|
||||||
|
# Token for github bot account
|
||||||
|
GitHubToken: xxxx
|
||||||
|
# Token for github bot account
|
||||||
|
GogsToken: xxxx
|
||||||
|
# Token for sonarcloud.io
|
||||||
|
SonarToken: xxxx
|
||||||
|
# Token for npmjs.org
|
||||||
|
NpmToken: xxxx
|
||||||
|
# Password Local NEXUS
|
||||||
|
NexusPassword: xxxx
|
||||||
|
# Password hub.docker.com
|
||||||
|
DockerHubPassword: xxxx
|
||||||
|
# Access key for saucelabs.com
|
||||||
|
SauceAccessKey: xxxx
|
||||||
|
File:
|
||||||
|
# Set to false to keep existing secret
|
||||||
|
Replace: true
|
||||||
|
# PGP Private key in ascii format used to sign artifacts
|
||||||
|
PGPPrivateKeyAsc: |-
|
||||||
|
-----BEGIN PGP PRIVATE KEY BLOCK-----
|
||||||
|
xxxxx
|
||||||
|
-----END PGP PRIVATE KEY BLOCK-----
|
||||||
|
# maven.settings file
|
||||||
|
MavenSettingsXML: |-
|
||||||
|
<settings>
|
||||||
|
<localRepository>${user.home}/.mvnrepository</localRepository>
|
||||||
|
<interactiveMode>false</interactiveMode>
|
||||||
|
<mirrors>
|
||||||
|
<mirror>
|
||||||
|
<id>nexus</id>
|
||||||
|
<mirrorOf>external:*</mirrorOf>
|
||||||
|
<url>http://nexus.molgenis-nexus:8081/repository/maven-central/</url>
|
||||||
|
</mirror>
|
||||||
|
</mirrors>
|
||||||
|
<servers>
|
||||||
|
<!-- for snapshot builds of the master -->
|
||||||
|
<server>
|
||||||
|
<id>sonatype-nexus-staging</id>
|
||||||
|
<username>molgenis</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
<server>
|
||||||
|
<id>local-nexus</id>
|
||||||
|
<url>http://nexus.molgenis-nexus:8081/repository/maven-snapshots/</url>
|
||||||
|
<username>admin</username>
|
||||||
|
<password>xxxxx</password>
|
||||||
|
</server>
|
||||||
|
<!-- for docker images-->
|
||||||
|
<server>
|
||||||
|
<id>registry.molgenis.org</id>
|
||||||
|
<username>admin</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
<server>
|
||||||
|
<id>registry.hub.docker.com</id>
|
||||||
|
<username>molgenisci</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
</servers>
|
||||||
|
</settings>
|
||||||
|
|
@ -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: 0.3.0
|
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
|
||||||
|
|
@ -79,44 +79,5 @@ Specify memory usage for Java JVM:
|
||||||
|
|
||||||
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.
|
||||||
|
|
||||||
## Persistence
|
|
||||||
You can enable persistence on your MOLGENIS stack by specifying the following property.
|
|
||||||
|
|
||||||
- ```persistence.enabled```
|
|
||||||
|
|
||||||
You can also choose to retain the volume of the NFS.
|
|
||||||
- ```persistence.retain```
|
|
||||||
|
|
||||||
The size and claim name can be specified per service. There are now two services that can be persist.
|
|
||||||
|
|
||||||
- MOLGENIS
|
|
||||||
- ElasticSearch
|
|
||||||
|
|
||||||
MOLGENIS persistent properties.
|
|
||||||
- ```molgenis.persistence.claim```
|
|
||||||
- ```molgenis.persistence.size```
|
|
||||||
|
|
||||||
ElasticSearch persistent properties.
|
|
||||||
- ```elasticsearch.persistence.claim```
|
|
||||||
- ```elasticsearch.persistence.size```
|
|
||||||
|
|
||||||
|
|
||||||
### Resolve you persistent volume
|
|
||||||
You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
|
|
||||||
|
|
||||||
```
|
|
||||||
kubectl get pv
|
|
||||||
```
|
|
||||||
|
|
||||||
You can now view the persistent volume claims and the attached volumes.
|
|
||||||
|
|
||||||
| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
|
|
||||||
| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
|
|
||||||
| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
|
|
||||||
| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
|
|
||||||
|
|
||||||
You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
|
||||||
When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
|
||||||
|
|
||||||
## Firewall
|
## Firewall
|
||||||
Is defined at cluster level. This chart does not facilitate firewall configuration.
|
Is defined at cluster level. This chart does not facilitate firewall configuration.
|
||||||
|
|
|
||||||
|
|
@ -81,7 +81,7 @@ questions:
|
||||||
- variable: molgenis.resources.requests.memory
|
- variable: molgenis.resources.requests.memory
|
||||||
label: Container memory reservation
|
label: Container memory reservation
|
||||||
default: 1250Mi
|
default: 1250Mi
|
||||||
description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
|
description: "Memory reservation for this MOLGENIS container"
|
||||||
type: enum
|
type: enum
|
||||||
options:
|
options:
|
||||||
- "1250Mi"
|
- "1250Mi"
|
||||||
|
|
@ -96,36 +96,4 @@ questions:
|
||||||
options:
|
options:
|
||||||
- "1g"
|
- "1g"
|
||||||
- "2g"
|
- "2g"
|
||||||
group: "Resources"
|
group: "Resources"
|
||||||
- variable: persistence.enabled
|
|
||||||
default: false
|
|
||||||
description: "Do you want to use persistence"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Persistence"
|
|
||||||
label: Persistence
|
|
||||||
show_subquestion_if: true
|
|
||||||
subquestions:
|
|
||||||
- variable: persistence.retain
|
|
||||||
default: false
|
|
||||||
description: "Do you want to retain the persistent volume"
|
|
||||||
type: boolean
|
|
||||||
label: Retain volume
|
|
||||||
- variable: molgenis.persistence.size
|
|
||||||
default: "30Gi"
|
|
||||||
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "30Gi"
|
|
||||||
- "50Gi"
|
|
||||||
- "100Gi"
|
|
||||||
label: Size MOLGENIS filestore
|
|
||||||
- variable: elasticsearch.persistence.size
|
|
||||||
default: "50Gi"
|
|
||||||
description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "50Gi"
|
|
||||||
- "100Gi"
|
|
||||||
- "200Gi"
|
|
||||||
label: Size for ElasticSearch data
|
|
||||||
|
|
@ -49,11 +49,6 @@ spec:
|
||||||
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||||
ports:
|
ports:
|
||||||
- containerPort: 8080
|
- containerPort: 8080
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: molgenis-nfs
|
|
||||||
mountPath: /home/molgenis
|
|
||||||
{{- end }}
|
|
||||||
livenessProbe:
|
livenessProbe:
|
||||||
httpGet:
|
httpGet:
|
||||||
path: /
|
path: /
|
||||||
|
|
@ -92,25 +87,10 @@ spec:
|
||||||
ports:
|
ports:
|
||||||
- containerPort: 9200
|
- containerPort: 9200
|
||||||
- containerPort: 9300
|
- containerPort: 9300
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: elasticsearch-nfs
|
|
||||||
mountPath: /usr/share/elasticsearch/data
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
resources:
|
resources:
|
||||||
{{ toYaml .resources | indent 12 }}
|
{{ toYaml .resources | indent 12 }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
|
|
||||||
{{- if .Values.persistence.enabled }}
|
|
||||||
volumes:
|
|
||||||
- name: molgenis-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.molgenis.persistence.claim }}
|
|
||||||
- name: elasticsearch-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.elasticsearch.persistence.claim }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
{{- with .Values.nodeSelector }}
|
{{- with .Values.nodeSelector }}
|
||||||
nodeSelector:
|
nodeSelector:
|
||||||
|
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.elasticsearch.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.elasticsearch.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
@ -1,19 +0,0 @@
|
||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.molgenis.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.molgenis.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
@ -25,15 +25,12 @@ molgenis:
|
||||||
javaOpts:
|
javaOpts:
|
||||||
maxHeapSpace: "1g"
|
maxHeapSpace: "1g"
|
||||||
resources:
|
resources:
|
||||||
limits:
|
limits:
|
||||||
cpu: 1
|
cpu: 1
|
||||||
memory: 1250Mi
|
memory: 1250Mi
|
||||||
requests:
|
requests:
|
||||||
cpu: 200m
|
cpu: 200m
|
||||||
memory: 1250Mi
|
memory: 1250Mi
|
||||||
persistence:
|
|
||||||
claim: molgenis-nfs-claim
|
|
||||||
size: 30Gi
|
|
||||||
services:
|
services:
|
||||||
opencpu:
|
opencpu:
|
||||||
host: localhost
|
host: localhost
|
||||||
|
|
@ -60,17 +57,8 @@ elasticsearch:
|
||||||
requests:
|
requests:
|
||||||
cpu: 100m
|
cpu: 100m
|
||||||
memory: 1Gi
|
memory: 1Gi
|
||||||
persistence:
|
|
||||||
claim: elasticsearch-nfs-claim
|
|
||||||
size: 50Gi
|
|
||||||
|
|
||||||
persistence:
|
nodeSelector: {}
|
||||||
enabled: false
|
|
||||||
retain: false
|
|
||||||
|
|
||||||
nodeSelector: {
|
|
||||||
deployPod: "true"
|
|
||||||
}
|
|
||||||
|
|
||||||
tolerations: []
|
tolerations: []
|
||||||
|
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Reference in New Issue