updated README and questions.yml

molgenis/README.md

@@ -6,8 +6,70 @@ This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
 
 - MOLGENIS
 
-## 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```
+
+### OpenCPU
+You can specify the location of the OpenCPU cluster by specifying this property:
+- ```molgenis.services.opencpu.host: localhost```
+
+## 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```
+
+
+
+
 
 
 ## Firewall
-Is defined
+Is defined at cluster level. This chart does not facilitate firewall configuration.

molgenis/questions.yml

@@ -7,7 +7,7 @@ questions:
   description: "Hostname for your stack"
   type: hostname
   required: true
-  group: "Services and Load Balancing"
+  group: "Load Balancing"
   label: Hostname
 - variable: molgenis.image.repository
   default: "registry.hub.docker.com"
@@ -17,63 +17,63 @@ questions:
   - "registry.hub.docker.com"
   - "registry.molgenis.org"
   required: true
-  group: "MOLGENIS"
+  group: "Version"
   label: Registry
 - variable: molgenis.image.tag
   default: "stable"
   description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Version"
   label: Version
-- variable: molgenis.services.opencpu.uriHost
+- variable: molgenis.services.opencpu.host
   default: ""
   description: "Specify the OpenCPU cluster"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: OpenCPU cluster
 - variable: molgenis.services.elasticsearch.clusterName
   default: "molgenis"
   description: "Set the index name of MOLGENIS"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: Elasticsearch clustername
 - variable: molgenis.services.elasticsearch.transportAddress
   default: "localhost:9300"
   description: "Set the transport address for the elasticsearch node communication port and low-level api (which we use)"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: Elasticsearch transport address
 - variable: molgenis.services.postgres.host
   default: "localhost"
   description: "Set the location of the postgres cluster"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: Postgres cluster location
 - variable: molgenis.services.postgres.scheme
   default: "molgenis"
   description: "Set the database scheme"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: Database scheme
 - variable: molgenis.services.postgres.user
   default: "molgenis"
   description: "Set user of the database scheme"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: Database username
 - variable: molgenis.services.postgres.password
   default: "molgenis"
   description: "Set the password of the database scheme"
   type: string
   required: true
-  group: "MOLGENIS"
+  group: "Services"
   label: Database password
 - variable: molgenis.resources.limits.cpu
   default: 1
@@ -85,7 +85,7 @@ questions:
   - "3"
   - "4"
   required: true
-  group: "MOLGENIS - Resource limits"
+  group: "Resources"
   label: CPU limit
 - variable: molgenis.resources.limits.memory
   default: 1250Mi
@@ -97,7 +97,7 @@ questions:
   - "2000Mi"
   - "2500Mi"
   required: true
-  group: "MOLGENIS - Resource limits"
+  group: "Resources"
   label: Memory limit
 - variable: molgenis.javaOpts
   default: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
@@ -106,5 +106,5 @@ questions:
   options:
   - "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
   - "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  group: "MOLGENIS - Resource limits"
+  group: "Resources"
   label: Java memory options

molgenis/templates/deployment.yaml

@@ -32,7 +32,7 @@ spec:
             - name: molgenis.home
               value: /home/molgenis
             - name: opencpu.uri.host
-              value: {{ .services.opencpu.uriHost }}
+              value: {{ .services.opencpu.host }}
             - name: elasticsearch.transport.addresses
               value: {{ .services.elasticsearch.transportAddresses }}
             - name: elasticsearch.cluster.name

molgenis/values.yaml

@@ -32,7 +32,7 @@ molgenis:
     memory: 1Gi
   services:
     opencpu:
-      uriHost: localhost
+      host: localhost
     elasticsearch:
       transportAddresses: localhost:9300
       clusterName: molgenis