Hi, I just went to try out some things with recount3 and found that there seems to be an issue with the default data location, resulting in the "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.".

I installed the most recent version of the package, but the default URL is the same and gives the same error. I noticed in project_homes() that it can only reach that error if curl says the URL doesn't exist, and sure enough the default URL that project_homes() builds, http://duffel.rail.bio/recount3/human/homes_index is sending an HTTP 302 redirect to http://idies.jhu.edu/recount3/data/human/homes_index but RCurl::url.exists() seems to not treat a 302 as a successful response and returns FALSE. Running project_homes(organism = "human", recount3_url = "http://idies.jhu.edu/recount3/data") works fine, as does available_projects(recount3_url = "http://idies.jhu.edu/recount3/data").

Presumably this is a temporary issue with duffel.rail.bio?

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