Deploy with Docker

Prerequisites

Docker provides a way to run applications securely isolated in a container, packaged with all its dependencies and libraries. To learn more on Docker, kindly refer here: Docker overview.

Make sure that you have the latest version of Docker installed on your machine. Get latest version

Notes for non-Linux systems

Usage instructions ##

In this example we use Docker Compose to spin up all the different containers for cBioPortal.

Quick Start

git clone https://github.com/cBioPortal/cbioportal-docker-compose.git
cd cbioportal-docker-compose
./init.sh
docker-compose up

You should now be able to see the cBioPortal website at http://localhost:8080

Import studies with:

docker-compose run cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o

Clear persistent data volumes with:

docker compose down -v

Comprehensive Start

Step 1 - Run Docker Compose

Download the git repo that has the Docker compose file and go to the root of that folder:

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

Then download all necessary files (seed data, example config and example study from datahub) with the init script:

./init.sh

Then run:

docker-compose up

This will start all four containers (services) defined here. That is:

  • the mysql database, which holds most of the cBioPortal data

  • the cBioPortal Java web app, this serves the React frontend as well as the REST API

  • the session service Java web app. This service has a REST API and stores session information (e.g. what genes are being queried) and user specific data (e.g. saved cohorts) in a separate mongo database

  • the mongo database that persists the data for the session service

It will take a few minutes the first time to import the seed database and perform migrations if necessary. Each container outputs logs to the terminal. For each log you'll see the name of the container that outputs it (e.g. cbioportal_container or cbioportal_session_database_container). If all is well you won't see any significant errors (maybe some warnings, that's fine to ignore). If all went well you should be able to visit the cBioPortal homepage on http://localhost:8080. You'll notice that no studies are shown on the homepage yet. Go to the next step to see how to import studies.

Notes on detached mode

If you prefer to run the services in detached mode (i.e. not logging everything to your terminal), you can run

docker-compose up -d

In this mode, you'll have to check the logs of each container manually using e.g.:

docker logs -f cbioportal_container

You can list all containers running on your system with

docker ps -a

Step 2 - Import Studies

To import studies you can run:

docker-compose run cbioportal metaImport.py -u http://cbioportal:8080 -s study/lgg_ucsf_2014/ -o

This will import the lgg_ucsf_2014 study into your local database. It will take a few minutes to import. After importing, restart the cbioportal web container:

docker-compose restart cbioportal

You can visit http://localhost:8080 again and you should be able to see the new study.

All public studies can be downloaded from https://www.cbioportal.org/datasets, or https://github.com/cBioPortal/datahub/. You can add any of them to the ./study folder and import them. There's also a script (./study/init.sh) to download multiple studies. You can set DATAHUB_STUDIES to any public study id (e.g. lgg_ucsf_2014) and run ./init.sh.

Step 3 - Customize your portal.properties file ###

The properties file can be found in ./config/portal.properties. Which was set up when running init.sh.

This properties file allows you to customize your instance of cBioPortal with e.g. custom logos, or point the cBioPortal container to e.g. use an external mysql database. See for a the properties documentation for a comprehensive overview.

If you would like to enable OncoKB see OncoKB data access for how to obtain a data access token. After obtaining a valid token use:

Step 4 - Customize cBioPortal setup

To read more about the various ways to use authentication and parameters for running the cBioPortal web app see the relevant backend deployment documentation.

On server systems that can easily spare 4 GiB or more of memory, set the -Xms and -Xmx options to the same number. This should increase performance of certain memory-intensive web services such as computing the data for the co-expression tab. If you are using MacOS or Windows, make sure to take a look at these notes to allocate more memory for the virtual machine in which all Docker processes are running.

More commands ##

For documentation on how to import a study, see this tutorial For more uses of the cBioPortal image, see this file

To Dockerize a Keycloak authentication service alongside cBioPortal, see this file.

Uninstalling cBioPortal ##

docker compose down -v --rmi all