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NIH-NCPI / NCPI_use_case_tracker

This repo is for tracking NCPI interoperability use cases.
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UC 10. SRA & Kids First DRC for Kids First & UDN co-analysis #10

Open NoopDog opened 3 years ago

NoopDog commented 3 years ago

Status: ACTIVE Platform contact; TBD Researcher contact: TBD (will ask Matt Wheeler) Next steps: requires moving BAM files into AWS hot storage at SRA for DRS accessibility. This use case also relies on RAS. Dataset: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001232.v3.p2

cottonva commented 3 years ago

Update:

Status: NCBI actively moving all files (BAMs) to hot AWS/SRA storage. Files become immediately accessible to DRS as they are moved into S3. Next steps: Seven Bridges development work to obtain RAS passports, present them to NCBI/SRA DRS server to access files in CAVATICA workspaces. Platform contact: Michele Mattioni and Kurt Rodarmer Researcher contact: Lisa Bastarache Dataset: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001232.v3.p2 Use Case: Enable researchers to pull genomic data files from Kids First and SRA together in one cloud-based workspace for combined analysis without downloading and uploading data. User will run workflows and other analysis to help solve pediatric undiagnosed UDN cases using variants represented in Kids First childhood cancer and/or structural birth defects datasets. One pager description: https://github.com/NIH-NCPI/NCPI_use_case_tracker/blob/main/one_pagers/UC10_InteroperabilityUDN.md NCPI use case link: https://github.com/NIH-NCPI/NCPI_use_case_tracker/issues Funding resources: Kids First DRC parent award

Next steps:

cottonva commented 3 years ago

https://github.com/NIH-Auth-Services/CIT-IAM-RAS/issues/56

jackDiGi commented 2 years ago

@mattions, I think we are very close to getting full approval from RAS, once the tabletop tests are done - can you please confirm here?

mattions commented 2 years ago

Yes -- that is correct

ianfore commented 1 year ago

Issues were discussed in this GA4GH Connect session about how the files in NCBI managed AWS storage are accessed/transferred by the Cavatica platform and how

Assignment by the platform of new DRS ids to objects that already have DRS ids surfaces in this use case. The issue should be addressed.

The RAS issues have been addressed on the requisite servers for some time. The use of those services, along with others relevant to the use case have been explored.

The specific notebook for this has not been shared due to its controlled access content. The notebooks differs from this one only in that it uses controlled access data. The server calls used are identical other than that they include the passport required for authorization.