Download Any Reference File by URL — download_reference

Caches a file from an arbitrary URL in the same way as download_reference() (no re-download when present, partial files removed on failure). Useful for annotations without a provider layout, such as the T2T consortium Liftoff files or CHESS releases.

Usage

download_reference_url(
  url,
  output_path = ":cache:",
  file_name = NULL,
  timeout_limit = 3600,
  method = "auto"
)

Arguments

url: URL of the file.
output_path: Directory where the file is saved; ":cache:" (the default) is the package cache.
file_name: File name to use; defaults to the last part of the URL.
timeout_limit: Maximum time in seconds for the download. Takes precedence over options("timeout"). Defaults to 3600.
method: Method used by utils::download.file(). Defaults to "auto".

Value

The full path to the file.

Examples

if (FALSE) { # \dontrun{
liftoff <- download_reference_url(paste0(
  "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/",
  "assemblies/annotation/chm13v2.0_RefSeq_Liftoff_v5.2.gff3.gz"
))
annot <- prepare_isoformic_annotation(liftoff)
annot
} # }