Data Submission step-by-step
Intended Audience
Section titled “Intended Audience”Anyone intending to upload data to a CanDIG instance.
Prerequisites
Section titled “Prerequisites”- Decent working knowledge of python, JSON, docker, data transformation
- [Optional] Locally running CanDIG stack for testing
- Production CanDIG stack with authorization as Site curator or Program curator of the program(s) you are planning to ingest
- Clinical data exported from your source database into a tabular format (CSVs or multi-tabbed xlsx)
- Genomic data files in s3, local or NFS mounted drive available to htsget_app docker container
- Linkage information between the sample registrations in the clinical data and the genomic data files
What stage of ingest are you up to?
Section titled “What stage of ingest are you up to?”Step 1. Prepare clinical dataPrepare your clinical data for ingest
Step 2. Register programsRegister the programs you intend to ingest.
Step 3. Ingest clinical dataIngest your clinical data.
Step 4. Prepare Genomic dataPrepare your genomic data for ingest.
Step 5. Link Genomic dataLink your clinical data to your genomic data.
I need helpGet help with all aspects of ingest.