Set up working directory with parameters.
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) {
# 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
}