Download .fna, .faa, .gff files for filtered BV-BRC genomes

Default and fast method="ftp"

retrieveGenomes(
  base_dir = ".",
  user_bacs,
  method = c("ftp", "cli"),
  image = "danylmb/bvbrc:5.3",
  skip_existing = TRUE,
  ftp_workers = 8L,
  cli_fasta_workers = 4L,
  cli_gff_workers = 4L,
  chunk_size = 50L,
  verbose = TRUE
)

Arguments

base_dir

Project root (results layout preserved).

user_bacs

Input label(s) used to locate per-selection DB path.

method

"ftp" (default) or "cli".

image

Docker image for CLI path (default "danylmb/bvbrc:5.3").

skip_existing

Logical; if TRUE, do not re-download genomes already complete. Default TRUE.

ftp_workers

Parallel workers for FTP path (default 8).

cli_fasta_workers

Parallel chunk containers for FASTA+GTO (default 4).

cli_gff_workers

Parallel chunk containers for GFF export (default 4).

chunk_size

Genomes per chunk container (default 50).

verbose

Verbose messages.

Value

Character vector of genome IDs with complete file sets on disk.

Details

Alternative path to bypass FTP: method="cli"