# Import data with Docker

# Import data instructions

This is an example to import a sample study: study_es_0. When trying to import other studies, please follow the same routine:

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

# Step 1 - 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 run \
    cbioportal \
    bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel1.txt'
docker-compose run \
    cbioportal \
    bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /cbioportal/core/src/test/scripts/test_data/study_es_0/data_gene_panel_testpanel2.txt'

# Step 2 - 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 run cbioportal metaImport.py -u http://cbioportal:8080 -s /cbioportal/core/src/test/scripts/test_data/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. Note that this study is included inside the cbioportal container. The process for adding a study that is outside of the container is similar. Just make sure to add the data files in the ./study folder. This folder is mounted as /study/ inside of 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 the first step 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.