Cannot Initialize CBP from Docker

[Rebecca Sansale]

Hi-- I originally posted this issue here: https://groups.google.com/g/cbioportal/c/Muac6bDffDc/m/VnWrYAA_AQAJ

but didnt get a response, so im making a new thread. In the last paragraph when I reference following "step 2", im referring to Ben's instructions from Oct 7 2025 (https://groups.google.com/g/cbioportal/c/Muac6bDffDc/m/B-FmC0sdAgAJ) :

Heres what im experiencing:

I have followed the instructions for Deploying CBP with Docker, but the SQL database never initializes properly. The code I run is the following:

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

cd cbioportal-docker-compose

./init.sh

docker compose up

the compose up command produces the following error that is repeated: 

cbioportal-container                   | mysqladmin ping -s -h -P3306 -u -p

cbioportal-container                   | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...

from there, i check the state of the containers:

docker compose ps

which initially yields:

NAME                                    IMAGE                              COMMAND                  SERVICE                       CREATED          STATUS                             PORTS

cbioportal-container                    cbioportal/cbioportal:6.4.1        "docker-entrypoint.s…"   cbioportal                    30 seconds ago   Up 29 seconds                      0.0.0.0:8080->8080/tcp, [::]:8080->8080/tcp

cbioportal-database-container           mysql:8.0                          "docker-entrypoint.s…"   cbioportal-database           30 seconds ago   Up 25 seconds (health: starting)  0.0.0.0:3306->3306/tcp, [::]:3306->3306/tcp

cbioportal-session-container            cbioportal/session-service:0.6.4   "/__cacert_entrypoin…"   cbioportal-session            30 seconds ago   Up 29 seconds                      

cbioportal-session-database-container   mongo:4.2                          "docker-entrypoint.s…"   cbioportal-session-database   30 seconds ago   Up 29 seconds                      27017/tcp

however, after some time the SQL container status changes to: (unhealthy)

I havent made any changes to the CBP files. Im running this exactly as specified in the instructions. I have tried uninstalling and re-installing both Docker and CBP. I have also removed containers and volumes as well as restarted the container as you specified above.

I followed the instructions you provided, and get stuck at step 2, the cbioportal database does exist, however it doesnt contain any tables. 

as requested, here is the output from the logs:

2026-02-05 13:33:41+00:00 [Note] [Entrypoint]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/cgds.sql

2026-02-05 13:33:41+00:00 [Note] [Entrypoint]: /usr/local/bin/docker-entrypoint.sh: running /docker-entrypoint-initdb.d/seed.sql.gz

Thanks for your help--

Rebecca

[Gaofei Zhao]

Hi, Rebecca

Based on what you described, this issue seems related to files not being downloaded correctly during initialization.

Before starting a new installation, could you please try the following steps:

1. Make sure your repository is up to date
   Pull the latest version of the docker-compose setup:
   https://github.com/cBioPortal/cbioportal-docker-compose

2. Remove old database files

   • Double-check that your data folder contains only init.sh

   • Double-check that your study folder contains only init.sh

3. Bring down existing containers and volumes
   Run the following command before starting a new installation:

   docker-compose down -v

4. Verify your .env file
   Make sure the image version is set correctly, for example:

   cbioportal/cbioportal:6.4.1

5. Follow the official installation instructions
   Start a fresh installation by following the steps here, after running ./init.sh, please confirm that both seed.sql.gz and cgds.sql exist under the /data folder.

⚠️ Important note: These steps may clear your existing database. If you’d prefer not to remove your current data, please let me know before proceeding and we can explore alternative options.

Let me know how it goes or if you have any questions along the way.

Best regards,
Gaofei

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[Rebecca Sansale]

Hi Gaofei-- 

I looked into my issue more and the SQL server actually initializes fine. This problem has to do with the docker-compose.yml file and the 'cancer_type' data. When I run 'docker compose ps', the docker-compose.yml file is used to check the status of the containers -- within this file, the health of the SQL database ("healthcheck") is defined as healthy only if there are 853 rows in the 'type_of_cancer' table. For some reason, my table only has 852 lines instead of 853, which yields an 'unhealthy' health status, making it seem as though theres a problem with the SQL db.