I am using this package BSgenome.Hsapiens.UCSC.hg38 in a container on a compute cluster without internet access. When using this package, it attempts to download data and fails:

Error in download.file(url, destfile, quiet = TRUE) :
  cannot open URL 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz'
Calls: seqlevelsStyle<- ... .fetch_chrom_sizes_from_UCSC_database -> fetch_table_dump_from_UCSC -> fetch_table_from_url
Execution halted

Is there a way to point to a local path? What is the best way to deal with such issues in an offline environment?

Update: Added more complete code.

This is my code for running Cicero on Seurat objects based on this Signac vignette.

library(Seurat)
library(Signac)
library(cicero)
library(BSgenome.Hsapiens.UCSC.hg38)
library(dplyr)

seqlevelsStyle(BSgenome.Hsapiens.UCSC.hg38) <- "NCBI"
seqnames(BSgenome.Hsapiens.UCSC.hg38) <- BSgenome.Hsapiens.UCSC.hg38@seqinfo@seqnames

sf <- readRDS(file.path(path,"seurat.rds"))
mo <- SeuratWrappers::as.cell_data_set(sf)
co <- make_cicero_cds(mo, reduced_coordinates = reducedDims(mo)$UMAP)

# get the chromosome sizes from the Seurat object
genome <- as.data.frame(seqinfo(BSgenome.Hsapiens.UCSC.hg38)) %>%
  tibble::rownames_to_column("chr") %>%
  select(chr,seqlengths) %>%
  slice(1:25)

conns <- run_cicero(co, genomic_coords = genome, sample_num = 100)
ccans <- generate_ccans(conns)
links <- ConnectionsToLinks(conns = conns, ccans = ccans)
Links(sf) <- links

It's going to need internet access. When you switch to NCBI seqlevels, you are calling this function

.fetch_chrom_sizes_from_UCSC_database <- function(genome,
    goldenPath.url=getOption("UCSC.goldenPath.url"))
{
    col2class <- c(chrom="character", size="integer", fileName="NULL")
    ans <- fetch_table_dump_from_UCSC(genome, "chromInfo",
                                      col2class=col2class,
                                      goldenPath.url=goldenPath.url)
    ## Some sanity checks that should never fail.
    in_what <- paste0("\"chromInfo\" table for UCSC genome ", genome)
    .check_chrom_sizes(ans, in_what)
    ans
}

Which is in the GenomeInfoDb package. If you had a local UCSC genome browser DB running, you could use that, but it would be easier to just modify the seqlevels on that BSgenome object on a laptop or whatever and save as an RDS object that you could then, uh, put on a thumb drive and plug into your airgapped computer?