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README.md
MOLGENIS
This chart is used for acceptance and production use cases.
Containers
This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
- MOLGENIS
- ElasticSearch
- PostgreSQL (optional)
Provisioning
You can choose from which registry you want to pull. There are 2 registries:
The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates).
The three properties you need to specify are:
molgenis.image.repository
molgenis.image.name
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
Firewall
Is defined at service level you can specify this attribute in the values:
molgenis.firewall.enabled
default 'false'
If set to 'true' the following options are available. One of the options below has to be set.
molgenis.firewall.umcg.enabled
default 'false'molgenis.firewall.cluster.enabled
default 'false'
UMCG = only available within the UMCG. Cluster = only available within the GCC cluster environment.
Services
When you start MOLGENIS you need:
- an elasticsearch instance (5.5.6)
- an postgres instance (9.6)
You can attach additional services like:
- an opencpu instance
Elasticsearch
You can configure elasticsearch by giving in the cluster location.
To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch. From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5.
molgenis.services.elasticsearch.transportAddresses: localhost:9300
To configure the index on a Elasticsearch cluster you can specify the clusterName property.
molgenis.services.elasticsearch.clusterName: molgenis
Postgres
You can specify the location of the postgres instance by specify the following property:
molgenis.services.postgres.host: localhost
You can specify the schema by filling out this property:
molgenis.services.postgres.scheme: molgenis
You can specify credentials for the database scheme by specifying the following properties:
molgenis.services.postgres.user: molgenis
molgenis.services.postgres.password: molgenis
To test you can use the PostgreSQL-helm chart of Kubernetes and specify these answers:
# answers for postgresql chart
postgresUser=molgenis
postgresPassword=molgenis
postgresDatabase=molgenis
persistence.enabled=false
OpenCPU
You can specify the location of the OpenCPU cluster by specifying this property:
molgenis.services.opencpu.host: localhost
You can test OpenCPU settings using the OpenCPU-helm chart of MOLGENIS.
Resources
You can specify resources by resource type. There are 2 resource types.
- memory of container
- maximum heap space JVM
Specify memory usage of container:
molgenis.resources.limits.memory
Specify memory usage for Java JVM:
molgenis.javaOpts.maxHeapSpace
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
default 'true'
You can also choose to retain the volume of the NFS.
persistence.retain
default 'false'
The size and claim name can be specified per service. There are now two services that can be persist.
- MOLGENIS
- ElasticSearch
- PostgreSQL (optional)
MOLGENIS persistent properties.
molgenis.persistence.claim
molgenis.persistence.size
ElasticSearch persistent properties.
elasticsearch.persistence.claim
elasticsearch.persistence.size
PostgreSQL persistent properties.
postgres.persistence.claim
postgres.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
.