Open mbarkley opened 3 years ago
There is a Seven Bridges WES script now thanks to #9
Great proposal. I think there's even value in running something against more than one Seven Bridges implementation. I'd like to revive this model of looking at a FASP script to highlight which aspects of federation it hits. In this case it would address those in bold. It also has the option that we can test federated authentication and authorization early.
Your list above would check all those.
Have updated FASPScript17 which runs a compute on TCGA and GTEx data in a single script. These come from different repositories and driver projects.
See GTEX_TCGA_Federated_Analysis notebook
There's now a PR sent to fix the DNAstack WES client. Tomorrow I'll start tinkering with an ELIXIR script.
Merged the PR. Now thinking of tinkering with running samtools via the DNAStack WES. The problem we hit with that last summer seemed to be the "requester pays" buckets.
Added DNAStackWESTour notebook to explore some more.
It looks like we may still have the requester pays problem, but otherwise the server looks in good shape.
I've sent PR #19 with an ELIXIR WES client implementation. I don't think I'll get to write a script using all the WES clients this week for a single federated workflow, but I think we're a lot closer now.
Raising the question whether the Federated VUS notebook addresses the intent of this issue. The link shown is the notebook that aggregates the results. Notebooks in the same folder show running the same workflow on three different instances of the Seven Bridges platform.
This...
Barriers to the latter are
Proposing that we close this issue and address those barriers. Perhaps via issues in this repo which are specific to those barriers, or by other means.
Thoughts @mbarkley ?
Motivation
A long-standing goal of the FASP GA4GH group has been to have a federated workflow demo that anyone can run. In this context, a federated workflow means:
Goals
Todo