Recount3 error with default "recount3_url" option
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@cornwell-adam-5680
Last seen 7 weeks ago
United States

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?

recount3 • 217 views
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Just got the same error. Right now it seems that http://idies.jhu.edu/recount3/data/human/homes_index doesn't work as well.

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@lcolladotor
Last seen 10 hours ago
United States

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

Thanks! Leo

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