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
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'
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
:warning: after importing a study, remember to restart
cbioportal-container to see the study on the home page. Run
docker restart cbioportal-container.
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.
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.
Please make sure the seed database was correctly imported.
Remember to restart the
cbioportal-container after data imported.
docker restart cbioportal-container
If you are importing GRCh38 data, please remember to add
-ncbi 38 in your importing data command. The
-ncbi is set to
37 by default, adding
-ncbi 37 is optional for importing GRCh37 data.
Description for other parameters can be found by running
docker-compose run cbioportal metaImport.py -h or following this link