This repository is the home of a cBioPortal version that was modified and extended for usage in a molecular tumor board.
Installation is described here
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.
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:
- Make a Backup of the HAPI FHIR database using
sudo docker-compose exec hapi-postgres pg_dumpall -U hapiserver > dump.sql
- Extract the hapi database using
sed '/\\connect hapi/,$!d' dump.sql > dump_hapi.sql
- Verify that the newly created
dump_hapi.sql
file looks alright. - Move the files
dump.sql
anddump_hapi.sql
as well the directoriesreports
andstudy
to a different location. - 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! - Delete the MTB-cbioportal directory and make a fresh clone of the git repository using
git clone https://github.com/buschlab/MTB-cbioportal.git
- Copy dump.sql and dump_hapi.sql to the MTB-cbioportal directory
- Start the Postgres database using
docker-compose up -d hapi-postgres
- Import the
dump_hapi.sql
using the following commanddocker-compose exec -T hapi-postgres psql -U hapiserver -d hapi < dump_hapi.sql
- Proceed with step 2 of the installation as shown in INSTALL.md
- OpenResty Reverse Proxy
- cBioPortal
- MariaDB Server
- cBioPortal Session Service
- Mongo DB
- FhirSpark
- HAPI FHIR Server
- PostgreSQL Server
- HAPI FHIR Server
- Genome Nexus
- Mongo DB
- Ensembl REST API
- MariaDB Server
- cBioPortal
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 of the backend can be done by attaching a debugger to it. For VisualStudio Code the MSKCC provides an example configuration.
All code from MTB-cBioPortal is published under the GNU AGPL v3 License.