TRE Documentation: All Of Us Researcher Workbench, UK Biobank Research Analysis Platform

[smlmbrt]

We're currently developing documentation with clear intsructions for how to run the pgsc_calc tool in specific trusted research environments (TRE). This includes:

• All Of Us (AoU) Researcher Workbench
• UK Biobank (UKB) Research Analysis Platform

We'll keep this ticket open for people who have insights or questions about the process.

[nebfield]

Draft instructions that describe using a single container image

[Fiwx]

Is it possible to run pgsc_calc, containerized, on All of Us? I would be interested in using pgsc_calc on these biobanks. However, I don't know of a way to run pgsc_calc inside of singularity on the All of Us platform, or if it is possible.

[smlmbrt]

@Fiwx, yes it is possible to run it inside a docker image and a single job. We are currently finalising some documentation to describe this process, and planning some future software updates that should make the pipeline easier to run in theses settings.

[Fiwx]

That's great! If you have any code or notebooks that are able to be shared on that, I would appreciate it, even if they're unfinished or not perfect. I've been trying to do that for a long time and haven't been able to figure it out.