cbioportal docker image doesn't contain importReferenceGenome script in /cbioportal/core/src/main/scripts

According to the Import Reference Genome docs, reference genomes can be imported via the importReferenceGenome.pl script, located in <your_cbioportal_dir>/core/src/main/scripts.

However, this script doesn't exist in the /cbioportal/core/src/main/scripts directory in a container running the cbioportal/cbioportal image.

Below is me connecting to the docker image via docker-compose, using the yml file from the cBioPortal/cBioPortal-docker-compose repo:

% docker-compose run --rm cbioportal /bin/bash
Starting cbioportal_session_database_container ... done
Starting cbioportal_database_container         ... done
Starting cbioportal_session_container          ... done
Creating cbioportal-docker-compose_cbioportal_run ... done

root@3ec4103bb946:/# ls /cbioportal/core/src/main/scripts/
addCaseList.pl                   convertGeneIds.pl                          hotDeploy.py                    importMutSig.pl                             mini_load_ova.sh
all-breast-su2c.sh               convertGeneSymbols.pl                      import-portal-users.sh          importPdbUniprotResidueMappingFromMA.pl     ovarian
all-coadread-public.sh           convertPdbUniprotMappingFromMaDb.py        import-prad-su2c-caises-xml.sh  importPdbUniprotResidueMappingFromSifts.pl  portal-client.py
all-gbm-public.sh                convertSvsImages.pl                        importAccessRights.pl           importPfamGraphicsData.pl                   prepareBasicPiHelperData.sh
all-lusc-public.sh               cutInvalidCases.pl                         importCancerStudy.pl            importPiHelperData.pl                       prepareCosmicData.sh
all-ovarian-public.sh            deleteAllCaseLists.pl                      importCaseList.pl               importProfileData.pl                        prepareEbiSiftsPdbUniprotMappingData.sh
all-ovarian-su2c.sh              downloadChromosomeSizes.py                 importCaseListData.pl           importProteinArrayData.pl                   prepareGeneData.sh
all-prostate-broad.sh            dumpPortalInfo.pl                          importClinicalData.pl           importSangerCensus.pl                       preparePathwayCommonsData.sh
all-prostate-mich.sh             env.pl                                     importCopyNumberSegmentData.pl  importSif.pl                                prepareSangerCGC.sh
all-prostate-mskcc.sh            env.sh                                     importCosmicData.pl             importTimelineData.pl                       prepareUniProtData.sh
all-prostate-su2c.sh             envSimple.pl                               importDrugData.pl               importTypesOfCancer.pl                      processPathwayCommonsInteractions.py
all-prostate-tcga.sh             exportProfile.pl                           importGenePanel.pl              importUniProtIdMapping.pl                   reload.sh
all-su2c.sh                      fetchBCRDataDict.sh                        importGenes.pl                  importUsers.py                              resetDb.pl
all-ucec-su2c.sh                 fetchPfamGraphicsData.sh                   importGenesetData.pl            importer                                    showAllCaseLists.pl
calculateCoExpression.pl         filterCases.pl                             importGenesetHierarchy.pl       init.sh                                     statDb.pl
calculateMutationFrequencies.py  filterCases.sh                             importGistic.pl                 loadNetwork.sh                              updateGenePanel.pl
compareDirectAndBulkDBMSload.pl  flagStudyForProductionPortalDeployment.py  importHprd.pl                   loadSampleData.sh                           updateMetaData.pl
convertCosmicVcfToMaf.pl         generateMutationData.pl                    importMicroRNAIDs.pl            massagePortalDataForCancerStudies.pl        verifyGeneSets.pl
convertExpressionZscores.pl      hot-deploy.sh                              importMicroRna.pl               migrate_db.py

Any help is appreciated!

cBioPortal / cbioportal

cbioportal docker image doesn't contain importReferenceGenome script in /cbioportal/core/src/main/scripts #7899