tmfev/transmart-db-manage repository overview

⁠Supported tags

• latest (Dockerfile⁠)

⁠tMDataLoader

The tMDataLoader⁠ is an open source software for uploading medical data into the research platform tranSMART⁠.

⁠HOWTO

WARNING: DROP=true will drop any tranSMART database Schema already installed.

⁠Start transmart-data-mange

Start this container with a link to an already running database instance of tmfev/transmart-db⁠.

• DROP: drops an already installed tranSMART Database
• UPLOAD: uploads two example studies

docker run --name transmart-db-manage -e "POSTGRES_PASSWORD=POSTGRESSPASSWORDCHANGEME" -e "DROP=false" -e "UPLOAD=true" --link transmart-db:transmart-db -t -i tmfev/transmart-db-manage

⁠Upload more example studies

Two example studies are automatically uploaded into the connected tranSMART database. To upload more example studies from Rancho BioSciences⁠ or Thomas Reuters⁠ either download the studies directly, uncompress them in "/opt/tMDataLoaderData/Public Studies/ and proceed with Upload your own data or edit the skript file.

vim /opt/upload_GSE_studies.sh

⁠Upload your own data

Place your data according to the tMDataLoader⁠-Guide in /opt/tMDataLoaderData and use the script /opt/upload.sh to upload your files.