downloading data onto a HPC that is locked off from the internet

[chrisclarkson]

Hello,
I have an issue that was initially outlined here

I work on a cluster that is closed off from the internet (which is obviously beyond your control)... which is making it difficult to use your package- I tried testing the initial ExperimentHub command:

and then again with localHub=T:

and so I tried downloading the sqlite database directly:

And it seems to have worked...

Looking inside the ~/.cache/R/ExperimentHub/ databases:

It seems that certain data might be missing from the resource table.
But the downloaded experimenthub.sqlite data seem to be intact(?):

Hence I am wondering if there is some way that I can just add the experimenthub data manually to your BiocFilecache database to get the package working for me....?

A lofty ask- I know- but appreciate any advice you can give.
Kind Regards

[lshep]

I won't have time to look at this in more detail for a week or two -- but my initial thoughts for you to try:

Being locked off from the internet would mean you wouldn't be able to download any resources anyways so using localHub=TRUE would not be ideal unless it has run once with internet to get the database as well as download any resources you want available for your research.

What I think would work , would be to create the experiment hub cache locally and look at the BiocFileCache for importing and exporting a cache -- https://bioconductor.org/packages/release/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#exporting-and-importing-cache -- I have created an import or export for experimenthub/annotationhub but maybe in this case it would be useful to implement as an enhancement