run | R Documentation |
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.
run(wd, nstages = 4)
wd |
Working directory |
nstages |
Number of total stages to run, max 4. |
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()
## 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]'
# e.g. "/usr/local/ncbi/blast/bin/"
setup(wd = wd, txid = 9504, ncbi_dr = ncbi_dr) # txid for Aotus primate genus
run(wd = wd)
## End(Not run)
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