setup: Set-up parameters

Description Usage Arguments Details See Also Examples

View source: R/pipeline.R

Description

Set up working directory with parameters.

Usage

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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

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## Not run: 
  
  # 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

## End(Not run)

ropensci/phylotaR documentation built on Jan. 16, 2020, 11:47 a.m.