Question

Unable to load data from duffel.rail

0

Entering edit mode

Max Bone • 0

@2c3c5d53

Last seen 8 months ago

United Kingdom

This code was running fine previously but now im unable to access any of the recount3 data. Is there something I'm doing wrong or is this a server issue?

library("recount3")

options(recount3_url = "http://duffel.rail.bio/recount3")
human_projects <- available_projects()

#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.

recount recountWorkflow recount3 • 1.6k views

ADD COMMENT • link updated 18 months ago by Leonardo Collado Torres ★ 1.1k • written 23 months ago by Max Bone • 0

1

Entering edit mode

Confirmed in both release and devel. I hope the maintainers are watching the support site. Could be a server error. Perhaps this part in the example

> ?available_projects
>      available_projects(
+          recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test"
+      )
2022-12-08 08:04:43 caching file sra.recount_project.MD.gz.
    project organism file_source     project_home project_type n_samples
1 ERP001942    human         sra data_sources/sra data_sources       667
2 DRP004088    human         sra data_sources/sra data_sources         2

will get you some mileage...

ADD REPLY • link 23 months ago Vincent J. Carey, Jr. 6.7k

0

Entering edit mode

Thanks Vince for checking on recent versions of recount3. Seems duplicated with https://github.com/LieberInstitute/recount3/issues/29.

ADD REPLY • link 23 months ago Leonardo Collado Torres ★ 1.1k

1

Entering edit mode

One of the SciServer (file host) admins can likely resolve this issue but is traveling today. So you might want to wait 24 hrs before trying again.

Best, Leo

(On vacation)

ADD REPLY • link 23 months ago Leonardo Collado Torres ★ 1.1k

score 0 · Answer 1 · 2022-12-14

0

Entering edit mode

Leonardo Collado Torres ★ 1.1k

@lcolladotor

Last seen 24 days ago

United States

Hi,

This issue has now been resolved as noted in more detail at https://github.com/LieberInstitute/recount3/issues/29#issuecomment-1350429902.

Thanks again for your report.

Best, Leo

ADD COMMENT • link 23 months ago Leonardo Collado Torres ★ 1.1k

score 0 · Answer 2 · 2023-01-11

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

score 0 · Answer 3 · 2023-05-06

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