Description Usage Arguments Details See Also Examples
Set up working directory with parameters.
1 |
wd |
Working directory |
txid |
Root taxonomic ID(s), vector or numeric |
ncbi_dr |
Directory to NCBI BLAST tools, default '.' |
v |
Verbose, T/F |
... |
Additional parameters |
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
().
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
|
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