restart: Restart a phylotaR pipeline run

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Restart a phylotaR pipeline run

Description

Restarts the running of a pipeline as started with run.

Usage

restart(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(), run(), setup(), taxise_run()

Examples

## Not run: 
  
  # 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]'
  setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr)  # txid for Aotus primate genus
  # run and stop after 10 seconds
  R.utils::withTimeout(expr = {
    run(wd = wd)
  }, timeout = 10)
  # use ctrl+c or Esc to kill without a timelimit
  # and restart with ....
  restart(wd = wd)

## End(Not run)

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.