Timeout was reached: [seurat.nygenome.org]

[zofieLin]

Hi, I wonder whether it possible to RunAzimuth() without network. I already download the reference (ref.Rds and idx.annoy) and run with a path
RunAzimuth(query = obj, reference = "/lustre1/azimuth_humanLiver")
Have test on my desktop and worked well, however, when submit the job to PBS without internet, it will showed the error messages below:

Error in curl::curl_fetch_memory():
! Timeout was reached: [seurat.nygenome.org] Failed to connect to seurat.nygenome.org port 443 after 10001 ms: Timeout was reached
Backtrace:

1. Azimuth::RunAzimuth(query = aggr.anno, reference = "/lustre1/azimuth_humanLiver")
2. Azimuth:::RunAzimuth.Seurat(query = aggr.anno, reference = "/lustre1/azimuth_humanLiver")
3. Azimuth::ConvertGeneNames(...)
4. Azimuth:::Online(url = homolog.table)
5. httr::GET(url = url, httr::timeout(seconds = getOption("timeout")))
6. httr:::request_perform(req, hu$handle$handle)
7. httr:::request_fetch.write_memory(req$output, req$url, handle)
8. curl::curl_fetch_memory(url, handle = handle)
   Execution halted

I wonder whether it have solution to make it work without using network?
Thanks.

[danielsarj]

Also having the same issue. The problem, as someone else has pointed out, is that the function accesses seurat.nygenome.org to obtain the homolog table, but the connection sometimes cannot be established.

It'd be helpful if, similarly for the reference, the user could provide a local path for the homolog table. Any words from the developers?