molgenis-ops-docker-helm/molgenis

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

Versions

You can choose from which registry you want to pull from. There are 2:

• https://registry.molgenis.org
• https://hub.docker.com

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

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 3 resource types.

• cpu's
• memory of container
• memory of JVM

Specify number of cpu's:

• molgenis.resources.limits.cpu

Specify memory usage of container:

• molgenis.resources.limits.memory

Specify memory usage for Java JVM:

• molgenis.javaOpts

Select the resources you need dependant on the customer you need to serve.

Firewall

Is defined at cluster level. This chart does not facilitate firewall configuration.