Importing test data with Docker

Instructions

This is an example to import the sample study study_es_0. study_es_0 is a testing and evaluation dataset that covers a broad range of cBioPortal data types. It is intended to help ensure that your cBioPortal importer is correctly handling all supported data types. We will follow this flow:

1. import gene sets (if applicable)
2. import gene panels (if applicable, studies without gene panels are assumed to be whole exome/genome)
3. import study data

Warning: Importing gene sets (Step 1) removes all existing gene set, gene set hierarchy, and gene set genetic profile data from the database. It is strongly recommended to do this on a fresh database instance rather than one that already contains geneset data you want to keep. Importing other studies may not work after importing study_es_0 and will require a fresh database to be loaded.

Step 1 - Import gene sets

study_es_0 relies on gene set data, so gene set definitions must be loaded before the study. Place the required reference files in the ./study/reference_data/ directory on the host (mounted as /study/reference_data/ inside the container), then run:

docker compose exec cbioportal importGenesetData.pl \
    --data /study/reference_data/study_es_0_genesets.gmt \
    --new-version msigdb_7.5.1 \
    --supp /study/reference_data/study_es_0_supp-genesets.txt

docker compose exec cbioportal importGenesetHierarchy.pl \
    --data /study/reference_data/study_es_0_tree.yaml

For studies that do not include gene set data, skip this step.

Step 2 - Import gene panels

To import gene panels for your study, please reference the example commands in this file

These are the commands for importing study_es_0 gene panels (data_gene_panel_testpanel1 and data_gene_panel_testpanel2):

docker compose exec cbioportal importGenePanel.pl --data /study/reference_data/data_gene_panel_testpanel1.txt

docker compose exec cbioportal importGenePanel.pl --data /study/reference_data/data_gene_panel_testpanel2.txt

Step 3 - Import data

To import data for your study, please reference the example commands in this file

Command for importing study_es_0 data:

docker compose exec cbioportal metaImport.py -s /study/study_es_0 -o

⚠️ after importing a study, remember to restart cbioportal to see the study on the home page. Run docker compose restart cbioportal.

You have now imported the test study study_es_0. The process for adding a study that is outside of the container is similar — place the data files in the ./study folder on the host, which is mounted as /study/ inside the container.

Frequently Asked Questions

Gene panel ID is not in database

If you see an error like this when you importing the data:
ERROR: data_gene_panel_matrix.txt: lines [2, 3, 4, (10 more)]: Gene panel ID is not in database. Please import this gene panel before loading study data.; values encountered: ['TESTPANEL1', 'TESTPANEL2']

please follow Step 2 to import gene panels (e.g. import data_gene_panel_testpanel1 and data_gene_panel_testpanel2 for study_es_0), then try to import the data again.

Error occurred during validation step

Please make sure the seed database was correctly imported.

Study imported correctly, but got error when trying to query something

Remember to restart the cbioportal after data imported.

docker compose restart cbioportal

Import GRCh38 data

If you are importing GRCh38 data, please remember to set the reference_genome: hg38 field in the meta_study.txt file. See also cancer study metadata.