How does one access TCGA controlled data in AWS S3?

Question

[Cmouli]

AWS Data Exchange for TCGA pages points to the existence of the S3 bucket tcga-2-controlled. Does anyone know how to download data from the bucket using the GDC Data access token that one needs to access the controlled data?

The page that is linked for details under controlled access does not mention AWS resource at all.

[Ram]

The page has an option to Request Access. Have you tried that?

[Cmouli]

Yes of course. I have access to dbGap and I usually use the GDC Data Transfer Tool to download the controlled data using authorization token. But I was looking for a way to directly access the aligned reads from the S3 bucket if that was possible.

[GenoMax]

Please ask GDC support. That may be the best option.

[Zhenyu Zhang]

Although the data source is from GDC, these AWS buckets are not managed by the GDC.

1. GDC does not have a way to let you directly access these buckets.
2. I know a lot of people access them via Broad Institute FireCloud/Terra or Cancer Genomics Cloud by Seven Bridges.

[Ram]

The AWS page says it's provided by https://ctds.uchicago.edu/. Maybe try emailing [e-mail]?

[Zhenyu Zhang]

I have told you the answers "Broad Institute FireCloud/Terra or Cancer Genomics Cloud by Seven Bridges"

[GenoMax]

Since you appear to be knowledgeable about this does this mean that those buckets are ONLY for use/access from Terra or SevenBridges? If that is the case then OP may need to give up on them.

[Zhenyu Zhang]

I heard that this was just implemented https://gen3.org/resources/user/gen3-client/ But you will need credentials from nci-crdc.datacommons.io as described in the documentation. However, there is not a direct bucket to bucket download.