Setting Up cBioPortal in MyDRE

Setting Up cBioPortal in MyDRE


If you're using a clean Linux VM and want to install cBioPortal manually:

1. Create the VMs in one workspace

  1. Add one default Windows VM and start it.
  2. Add a standard Linux Ubuntu 22 VM and start it.

2. Whitelist Required URLs

Whitelist the following domains under External Access settings in myDRE:

github.com
raw.githubusercontent.com
packages.microsoft.com
azure.archive.ubuntu.com
docker.com
docker.io
cbioportal-datahub.s3.amazonaws.com (only needed for example dataset)
oncokb.org
civicdb.org/
genomenexus.org
gsea-msigdb.org
oncotree.mskcc.org

3. Prepare and Upload Scripts

Since copy-paste is not possible inside the VM, we will prepare scripts in advance and upload them using the Files feature in myDRE.

Upload the following files:

a. install_docker.sh

#!/bin/bash

# Add Docker's official GPG key:
sudo apt-get update sudo apt-get install ca-certificates curl
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc

# Add the repository to Apt sources:
echo \
      "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu \
      $(. /etc/os-release && echo "${UBUNTU_CODENAME:-$VERSION_CODENAME}") stable" | \
sudo tee /etc/apt/sources.list.d/docker.list > /dev/null sudo apt-get update sudo apt-get install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

# Adds current user to docker security group
sudo groupadd -f docker
sudo usermod -aG docker $USER
newgrp docker

b. configuration.sh 

[Service]
Environment="HTTP_PROXY=http://proxy.mydre.org:3128"
Environment="HTTPS_PROXY=http://proxy.mydre.org:3128"
Environment="NO_PROXY=localhost,127.0.0.1"

c. install_cbioportal.sh 

mkdir -p ~/cbioportal
cd ~/cbioportal
git clone https://github.com/cBioPortal/cbioportal-docker-compose.git
cd cbioportal-docker-compose

./init.sh
docker compose up

4. Connect to VMs

RDP into the Windows VM (log in with your @mydre.nl account).
Follow the SSH instructions here to connect to the Linux VM within the windows VM

5. Install Docker on Linux VM

  1. On the Linux VM, navigate to the Z: drive (mounted file share).
  2. Run the Docker installation script:  ./install_docker.sh
  3. Enter your sudo password when prompted.

6. Configure Docker Proxy

To route Docker traffic through the MyDRE proxy:

  1. Create a docker proxy settings file 

    1. sudo mkdir -p /etc/systemd/system/docker.service.d/
    2. sudo nano /etc/systemd/system/docker.service.d/http-proxy.conf

  2. Paste the contents of configuration.sh into the file (exit and save) 

  3. Then apply the changes:

    1. sudo systemctl daemon-reload
    2. sudo systemctl restart docker

  4. Verify that docker is running and check with  hello world

    1. sudo systemctl status
    2. docker docker run hello-world

7. Install cbioportal

Notes
This step may take a while to complete.
RUN  install_cbioportal.sh from home folder 

8. Enable VM Communication

To allow communication between the Windows and Linux VMs in the same Workspace. Add the Linux VM’s IP address to the Windows proxy exception list: (Windows menu → Settings → Network & Internet → Proxy) 

9. Access cBioPortal in Browser

From the Windows VM:
  1. Open Google Chrome.
  2. Navigate to:
    1. http://<linux-vm-ip>:8080
    2. Replace <linux-vm-ip> with the actual IP of your Linux VM.