Running V-Pipe on ELIXIR On Cloud (downstream processing)

[gordonkoehn]

Why

V-Pipe runs the Swiss national program to monitor viral variants (Sars-CoV-2, RSV and Influenza-A/B).
It has so far been deployed in cluster settings and we'll bring it to the cloud for more dynamic interactions.

What

• Fetch V-Pipe pre-processed output
• Run On-Demand, user-specified request for identifying new viral variariant dynamics using Lollipop

How

• Deployment: Docker on Compute Instance
• Pure Python
• Frontend: e.g. Streamlit or similar

Task List:

• Front-End: Static Mutation Heatmaps #9
• Front-End: Dynamic Mutation Heatmaps #10
• Containerize Lollipop, with the capability to read from S3 / fetch #13
• Front-End: Static Variant Evolution #12
• Front-End: On-Demand User-specified Variant Deconvolution #15
• Deploy on Compute Instance, S3 input/output #14

[gordonkoehn]

Let's defined the next goals.