Set up working directory with parameters.

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

Examples

if (FALSE) { # 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 }