Run phylotaR pipeline

Run the entire phylotaR pipeline. All generated files will be stored in the wd. The process can be stopped at anytime and restarted with restart. nstages must be a numeric value representing the number of stages that will be run. Stages are run in the following order: 1 - taxise, 2 - download, 3 - cluster and 4 - cluster2.

For example, specifying nstages = 3, will run taxise, download and cluster. Stages can also be run individually, see linked functions below.

Usage

run(wd, nstages = 4)

Arguments

wd

Working directory

nstages

Number of total stages to run, max 4.

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(), setup(), taxise_run()

Examples

if (FALSE) { # \dontrun{
  
  # Note: this example requires BLAST and internet 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
  run(wd = wd)
} # }