MTB-cbioportal

This repository is the home of a cBioPortal version that was modified and extended for usage in a molecular tumor board.

Installation

Installation is described here

Building images yourself

All images with a ghcr.io/buschlab/ prefix can be rebuilt using the following command:

sudo docker-compose -f compose-dev.yml build <service>

Such are marked in the table down below.

Upgrading from previous releases

When upgrading MTB-cBioPortal we highly suggest that you purge all volumes as it is likely that the database server is upgraded to a new major version and the cBioPortal seed database has been updated. This will result in a complete loss of all data that hasn't been backed up before! As cBioPortal loads it's data from disk, you should still have this saved on disk. You can import the data again in the new version.

The only part that needs a database backup is the HAPI FHIR server. For that please follow these steps:

1. Make a Backup of the HAPI FHIR database using sudo docker-compose exec hapi-postgres pg_dumpall -U hapiserver > dump.sql
2. Extract the hapi database using sed '/\\connect hapi/,$!d' dump.sql > dump_hapi.sql
3. Verify that the newly created dump_hapi.sql file looks alright.
4. Move the files dump.sql and dump_hapi.sql as well the directories reports and studyto a different location.
5. Stop all services of MIRMTBACUM-cbioportal using docker-compose down -v This will permanently delete all volume data, so you now rely on the backup you created in step 1!
6. Delete the MTB-cbioportal directory and make a fresh clone of the git repository using git clone https://github.com/buschlab/MTB-cbioportal.git
7. Copy dump.sql and dump_hapi.sql to the MTB-cbioportal directory
8. Start the Postgres database using docker-compose up -d hapi-postgres
9. Import the dump_hapi.sql using the following command docker-compose exec -T hapi-postgres psql -U hapiserver -d hapi < dump_hapi.sql
10. Proceed with step 2 of the installation as shown in INSTALL.md

Components

• OpenResty Reverse Proxy
  • cBioPortal
    • MariaDB Server
    • cBioPortal Session Service
      • Mongo DB
  • FhirSpark
    • HAPI FHIR Server
      • PostgreSQL Server
  • Genome Nexus
    • Mongo DB
    • Ensembl REST API
      • MariaDB Server

Ports

Service	Path (behind OpenResty)	Port (compose-dev.yml)	Image
OpenResty	/	8080	ghcr.io/buschlab/cbioroxy
cBioPortal	/	8081	ghcr.io/buschlab/cbioportal
cBioPortal Debugger	-	5005	-
cBioPortal DB	-	3306	mariadb
Session Service	-	5000	cbioportal/session-service
Session Service DB	-	27017	mongo
FhirSpark	/mtb/	3001	ghcr.io/buschlab/fhirspark
HAPI FHIR Server	/fhir/	8082	hapiproject/hapi
PostgreSQL Server	-	5432	postgres
Genome Nexus	/genome-nexus	8888	ghcr.io/buschlab/genome-nexus
Genome Nexus DB	-	27018	genomenexus/gn-mongo
Ensembl REST API	-	8083	nr205/ensembl-rest
Ensembl REST API DB	-	-	ghcr.io/buschlab/ensembl-mysql

Debugging

Debugging of the backend can be done by attaching a debugger to it. For VisualStudio Code the MSKCC provides an example configuration.

License

All code from the Data Sharing Framework is published under the GNU AGPL v3 License.