Import Study Using Docker

⚠️ Every time you add/remove/overwrite a study, please restart the Docker container with docker compose restart cbioportal.

Adding a Study

First, make sure that the study has been placed in the study/ directory under the cbioportal-docker-compose repo. Then open a terminal in the repo root and run:

docker compose exec cbioportal metaImport.py -s /study/<your_study> -o

Where:

• <your_study>: Replace with the subdirectory name in cbioportal-docker-compose/study/ containing the study's meta and data files.

For example, to import a study placed in cbioportal-docker-compose/study/my_study/:

docker compose exec cbioportal metaImport.py -s /study/my_study/ -o

Importing Multiple Studies

If importing multiple studies in a batch, skip the derived table rebuild after each import to save time:

docker compose exec cbioportal metaImport.py --no-derive-tables -s /study/my_study1/ -o
docker compose exec cbioportal metaImport.py --no-derive-tables -s /study/my_study2/ -o
docker compose exec cbioportal metaImport.py --no-derive-tables -s /study/my_study3/ -o

After all imports are complete, rebuild derived tables just once:

docker compose exec cbioportal metaImport.py derive-tables

Refer to the ClickHouse guide for more information on derived tables.

Restarting the Portal

After importing, restart the cBioPortal web container to clear the cache and see the new study:

docker compose restart cbioportal