Description Usage Arguments See Also Examples
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.
1 | 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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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