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:
- import gene panels (if applicable, studies without gene panels are assumed to be whole exome/genome)
- 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 (
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
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
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.