Merge pull request #11232 from zainasir/helm-docs

Add setup guide for Kubernetes deployment

.gitignore

@@ -109,3 +109,4 @@ Dockerfile.local
 security.properties
 *.crt
 *.key
+*~

docs/Downloads.md

@@ -32,7 +32,7 @@ TCGA Provisional studies often contain many different data types. These are exce
 
 #### Complete cBioPortal database
 
-A MySQL database dump of the complete cbioportal.org database can be found here: http://download.cbioportal.org/mysql-snapshots/public-portal-dump.latest.sql.gz
+A MySQL database dump of the complete cbioportal.org database can be found here: https://public-db-dump.assets.cbioportal.org/
 
 #### Seed Database
 

docs/SUMMARY.md

@@ -26,6 +26,7 @@
     * [Importing the Seed Database](deployment/deploy-without-docker/Import-the-Seed-Database.md)
     * [Deploying the Web Application](deployment/deploy-without-docker/Deploying.md)
     * [Loading a Sample Study](deployment/deploy-without-docker/Load-Sample-Cancer-Study.md)
+  * [Deploy on Kubernetes](deployment/kubernetes/README.md)
   * [Authorization and Authentication](deployment/authorization-and-authentication/README.md)
     * [User Authorization](deployment/authorization-and-authentication/User-Authorization.md)
     * [Authenticating Users via SAML](deployment/authorization-and-authentication/Authenticating-Users-via-SAML.md)

docs/deployment/README.md

@@ -4,6 +4,8 @@ Private instances of cBioPortal are maintained by institutions and companies [ar
 
 An instance can be deployed using Docker **(recommended)** or by building and deploying from source. The source code of cBioPortal is [available](https://github.com/cBioPortal/cbioportal) on GitHub under the terms of [Affero GPL V3](https://www.gnu.org/licenses/agpl-3.0.en.html).
 
-This section contains instructions for both of these paths.
+To deploy cBioPortal instance on a Kubernetes cluster, we also provide [official Helm charts](https://artifacthub.io/packages/search?org=cbioportal). You can follow the installation guide [here](./kubernetes/README.md).
+
+This section contains instructions for all of the above paths.
 
 Please note that installing a local version requires system administration skills; for example, installing and configuring Tomcat and MySQL. With limited resources, we cannot provide technical support on system administration.

docs/deployment/kubernetes/README.md

@@ -0,0 +1,71 @@
+# Deploy on Kubernetes
+
+## Prerequisites
+
+Official [cBioPortal Helm chart](https://artifacthub.io/packages/search?org=cbioportal) can be used to easily deploy an instance on a Kubernetes cluster. Make sure you meet the following prerequisites before continuing with the usage instructions:
+
+- You have access to a cluster (e.g. Minikube or AWS EKS). We recommend [setting up a Minikube cluster](https://minikube.sigs.k8s.io/docs/start/) on your local machine for development purposes.
+- You have installed [Helm](https://helm.sh/docs/intro/install/) on your system.
+- You have read and write access to a mysql database server.
+
+## Usage instructions
+
+
+### Cluster & Database Setup
+
+#### Step 1 - Add cBioPortal label to your cluster
+
+Make sure your cluster is already set up and you have access to a node running on it. Instructions for this can vary, depending on your Kubernetes provider. Once your cluster is active, run the following command to add a label to the node on your cluster.
+
+```
+kubectl label nodes <your-node-name> node-group=cbioportal
+```
+
+#### Step 2 - Export database access credentials
+cBioPortal needs access to a mysql database server hosting cancer study data. As mentioned in the prerequisites, you need access to a mysql database server for this. Instructions for this can vary, depending on your database server provider. Once you have a server available, download MSK's latest database dump [here](https://public-db-dump.assets.cbioportal.org/) and add the data to your database server. Then, continue with the instructions below using your mysql server credentials.
+
+Create a new values file called _values.secret.yaml_ and add your database credential values.
+```yaml
+container:
+    env:
+        - name: DB_USER
+          value: <your-db-user>
+        - name: DB_PASSWORD
+          value: <your-db-password>
+        - name: DB_CONNECTION_STRING
+          value: <your-db-connection_string>
+```
+
+### Install cBioPortal
+
+Now that your cluster and data sources have been successfully configured, you can install the cBioPortal helm chart.
+
+#### Step 1 - Install Helm Chart
+
+Add repository.
+```
+helm repo add cbioportal https://cbioportal.github.io/cbioportal-helm/
+```
+
+Install chart
+```
+helm install my-cbioportal cbioportal/cbioportal --version 0.1.6 -f path/to/values.secret.yaml
+```
+
+You should see something similar to this, indicating that the installation was successful.
+```
+NAME: my-cbioportal
+LAST DEPLOYED: Thu Nov 14 14:15:18 2024
+NAMESPACE: default
+STATUS: deployed
+REVISION: 1
+TEST SUITE: None
+```
+
+#### Step 2 - Access cBioPortal through localhost
+Run the following command to port-forward cBioPortal from the cluster to your local network.
+```
+kubectl port-forward deployment/cbioportal 10000:8080
+```
+
+cBioPortal should now be available at localhost on port 10000. Navigate to [http://localhost:10000](http://localhost:10000) in your browser to view it.