Example Commands

Importing gene panel ###

Use this command to import a gene panel. Specify the gene panel file by replacing <path_to_genepanel_file> with the absolute path to the gene panel file. Another option is to add the gene panel files in ./study which is mounted inside the container on `/study/.

docker-compose run \
-v <path_to_genepanel_file>:/gene_panels/gene_panel.txt:ro \
cbioportal
bash -c 'cd /cbioportal/core/src/main/scripts/ && ./importGenePanel.pl --data /gene_panels/gene_panel.txt'

Importing data ###

Use this command to validate a dataset. Add the study to the ./study folder. The command will connect to the web API of the container cbioportal-container, and import the study in its associated database. Make sure to replace <path_to_report_folder> with the absolute path were the html report of the validation will be saved.

docker-compose run \
-v "<path_to_report_folder>:/report" \
cbioportal \
metaImport.py -u http://cbioportal:8080 -s /study/name_of_study --html=/report/report.html

:warning: after importing a study, remember to restart cbioportal-container to see the study on the home page. Run docker-compose restart cbioportal.

Using cached portal side-data ####

In some setups the data validation step may not have direct access to the web API, for instance when the web API is only accessible to authenticated browser sessions. You can use this command to generate a cached folder of files that the validation script can use instead. Make sure to replace <path_to_portalinfo> with the absolute path where the cached folder is going to be generated.

docker-compose run \
-v "<path_to_portalinfo>/portalinfo:/portalinfo" \
-w /cbioportal/core/src/main/scripts \
cbioportal \
./dumpPortalInfo.pl /portalinfo

Then, grant the validation/loading command access to this folder and tell the script it to use it instead of the API:

docker-compose run \
-v "<path_to_report_folder>:/report" \
-v "<path_to_portalinfo>/portalinfo:/portalinfo:ro" \
cbioportal \
metaImport.py -p /portalinfo -s /study --html=/report/report.html

Inspecting or adjusting the database ###

docker-compose run cbioportal_database \
sh -c 'mysql -hcbioportal_database -u"$MYSQL_USER" -p"$MYSQL_PASSWORD" "$MYSQL_DATABASE"'

Deleting a study ###

To remove a study, run:

docker-compose run \
cbioportal \
cbioportalImporter.py -c remove-study -id study_id

Where study_id is the cancer_study_identifier of the study you would like to remove.