Data Submission step-by-step

Anyone intending to upload data to a CanDIG instance.

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

Step 1. Prepare clinical data Prepare your clinical data for ingest

Step 2. Register programs Register the programs you intend to ingest.

Step 3. Ingest clinical data Ingest your clinical data.

Step 4. Prepare Genomic data Prepare you genomic data for ingest.

Step 5. Link Genomic data Link your clinical data to your genomic data.

I need help Get help with all aspects of ingest.