Multi-Stack Demo for Oct 16th Breakout (can we combine a few breakouts?)

[briandoconnor]

Description

I think we should have a breakout that spans both days that focuses on what needs to be done between now and Oct 1st (or so) leading up to the final phase 1 Oct 16th demo.

To see details of the plan the full stacks are putting together see the Multi Team - End-of-pilot (October) Full Stack Demo Script

Topics should include some of the big issues we're facing and could best be solved by the full stacks working in the same room:

• [x] First step, just recap the current plan for those unfamiliar with the doc above, review our timeline (internal demo due Oct 1st)
• [x] Getting access for TOPMed/GTEx/MOD data on Google (see https://github.com/dcppc/2018-august-workshop/issues/15)
• [x] Confirm which group is doing which part of the overall compute
• [x] Testing the alignment and variant calling workflows provided by TOPMed and ported to WDL by Calcium and CWL by Xenon
• [x] Sharing analysis results from stack to stack with DOS (see https://github.com/dcppc/2018-august-workshop/issues/14)
• [x] Timeline
• [x] Identifying users from each stack and onboarding them into other stacks, retrieving an access token for use with DOS to access results from the cross stack compute
• [x] get together with KC2 and KC6 by the end of this, what do we implement?
• [x] working on our "messaging" for the presentation to the IC directors
  • what are the hard-problems we're trying to solve in Commons? Link to the use cases here.
  • what have we built in phase 1 and to address these hard problems?
  • what is our plan in phase 2 for addressing/continuing to address these hard problems
• More questions for discussion:
  • [ ] Will we have some subset of metadata harmonized on the TOPMed and GTEx samples, in a form that can be exchanged between the full stacks?
  • [ ] Will we do variant calling at each full stack or on a single full stack?
  • see more here

Type and size of room desired (conference room or lounge)

16

Target audience

Full stacks

[briandoconnor]

@raynamharris can you add the labels "fullstack" and "breakout"? Thanks

[djsz]

@raynamharris I think this would be a really valuable use of time!

[raynamharris]

Thanks, Brian! This is a great suggestion. Before I close the other issues, let's just confirm with @keanderka (who proposed #14 and #15) that it is okay to merge them into one large two-day discussion rather than keeping them separate.

[keanderka]

Hi @raynamharris - yes, let's combine them! I agree that these topics need a lot of work and will benefit from a wider scope during the breakout session.

[keanderka]

@raynamharris I made a Zoom invitation for this as I have some folks at Broad that will need to join remotely

Topic: Multi-stack Oct Demo - Breakout Session Time: Aug 27, 2018 1:00 PM Central Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android: https://broadinstitute.zoom.us/j/290865244

Or iPhone one-tap : US: +16465588656,,290865244# or +16468769923,,290865244# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 646 558 8656 or +1 646 876 9923 Meeting ID: 290 865 244 International numbers available: https://zoom.us/u/cDmt1x1Ka

[rpwagner]

@briandoconnor et al., can we keep the DOS and data access portion of this for tomorrow? The KC6 auth breakout is today (Day 1) and I need to be there. @madduri and @sulakhe will be available today to work on other topics.