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'
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
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
⚠️ after importing a study, remember to restart
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
study_id is the
cancer_study_identifier of the study you would like to remove.