Hello, I am trying to manually download data from the recount3 resource ( https://jhubiostatistics.shinyapps.io/recount3-study-explorer/ ), and I obtain the following error:

"ERROR: An error has occurred. Check your logs or contact the app author for clarification"

Using a query from R (using an old chunk of code) gives another error:

library("recount3")

gse = recount3::create_rse_manual(
    project = "BRCA",
    project_home = "data_sources/tcga",
    organism = "human",
    annotation = "gencode_v26",
    type = "gene"
)

Error: 'recount3_url' is not a valid supported URL since it's missing the URL/<organism>/homes_index text file or 'recount3_url' is not an existing directory in your file system.

Maybe this is an issue with the provider service? Or am I missing something?

Thank you

Hi,

Thank you for your interest in recount3 (and recount2).

We've been documenting this issue at https://github.com/LieberInstitute/recount3/issues/29. The IDIES link you were using changed recently to https://sciserver.org/public-data/recount3/data. However, we now have a new (2nd) host thanks to AWS at https://registry.opendata.aws/recount/. This is now the default host used by our load balancer duffel (https://github.com/nellore/digitalocean-duffel). recount3 version 1.9.1 documents these new hosts https://github.com/LieberInstitute/recount3/commit/6cf18f316123695b6a93c2049ab499b00d6c2acf.

Note that you need TLS version 1.2 or newer which most people have. If you encounter any new issues, please let us know at https://github.com/LieberInstitute/recount3/issues.

Please help us share this announcement

Very happy day for the recount project (https://t.co/U6IqgxYHaI) as @awscloud now hosts our data through their Open Data program. By default, we now direct downloads to S3 URLs starting with https and pointing into a recount-opendata bucket. 1/2

— @benlangmead@genomic.social (@BenLangmead) January 11, 2023

Thanks! Leo

Hi again,

If you are a Windows user, duffel now fully works on that operating system. That is, the duffel access issue has now been addressed by the internal switch from RCurl::url.exists() to httr::http_error(). You can gain access to these updates by installing recount3 version 1.10.2 (bioc-release aka 3.17) or 1.11.2 (bioc-devel aka 3.18).

duffel currently points to https://registry.opendata.aws/recount/ instead of IDIES.

Best, Leo