Set-up parameters

Set up working directory with parameters.

Usage

setup(
  wd,
  txid,
  ncbi_dr = ".",
  v = FALSE,
  overwrite = FALSE,
  outsider = FALSE,
  ...
)

Arguments

wd

Working directory

txid

Root taxonomic ID(s), vector or numeric

ncbi_dr

Directory to NCBI BLAST tools, default '.'

v

Verbose, T/F

overwrite

Overwrite existing cache?

outsider

Run through outsider? T/F

...

Additional parameters

Details

See parameters() for a description of all parameters and their defaults. You can change parameters after a folder has been set up with parameters_reset().

See also

Other run-public: ClstrArc-class, ClstrRec-class, Phylota-class, SeqArc-class, SeqRec-class, TaxDict-class, TaxRec-class, clusters2_run(), clusters_run(), parameters_reset(), reset(), restart(), run(), taxise_run()

Examples

if (FALSE) { # \dontrun{
  
  # Note: this example requires BLAST to run.
  
  # example with temp folder
  wd <- file.path(tempdir(), 'aotus')
  # setup for aotus, make sure aotus/ folder already exists
  if (!dir.exists(wd)) {
    dir.create(wd)
  }
  ncbi_dr <- '[SET BLAST+ BIN PATH HERE]'
  # e.g. "/usr/local/ncbi/blast/bin/"
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  # see ?parameters for all available parameter options
} # }