Commit 3e29e97d authored by Bertjan Broeksema's avatar Bertjan Broeksema

Allign preparation for wrighton

We have now all the files to prepare the wrighton dataset, as well as the
script to perform the preparation and to start the application.

This should users give a good deal of information to prepare their own
datasets.
parent 60fb2467
#setwd("~/icobire-guide")
# Adapt this path to the location in which you cloned the ICoVeR project from
# github.
#setwd("~/ICoVeR")
source("R.preprocessing/FrequenciesSignatures.R")
source("R.preprocessing/SymmetrizedSignatures.R")
source("R.preprocessing/ExtractESCG.R")
source("R.preprocessing/PrepareDataForInteractiveBinning.R")
# Prepare the CSTR data set
PrepareDataForInteractiveBinning(
dataset.name = "cstr",
file.fasta = "data//cstr_assembled.fasta",
file.abundance = "data//cstr_avg_coverage.csv",
file.escg = "data/cstr_escg.csv",
file.clusterings = "data//cstr_clusterings.csv",
dir.result = "R.ICoBiRe//data"
)
# Prepare the Wrighton data set
PrepareDataForInteractiveBinning(
dataset.name = "wrighton",
file.fasta = "data//wrighton_assembled.fasta",
file.abundance = "data//wrighton_avg_coverage.csv",
file.fasta = "data//wrighton_assembly.fasta.gz",
file.abundance = "data//wrighton_avg_cov.csv",
file.escg = "data//wrighton_escg.csv",
file.clusterings = "data//wrighton_clusterings.csv",
dir.result = "R.ICoBiRe//data"
dir.result = "R.ICoVeR//data"
)
#library(devtools)
#install_local(file.path(getwd(), "R.ICoBiRe"))
# Install the ICoVeR package after data generation.
# NOTE: Before running install_local, make sure that R.ICoVeR/R/sqlite.R
# is configured properly. The variable p.db.dataset must be assigned the
# same value as the value passed to dataset.name in
# PrepareForInteractiveBinning.
library(devtools)
install_local(file.path(getwd(), "R.ICoVeR"))
# Start opencpu and launch ICoVeR in the browser
library(opencpu)
opencpu$stop() # It starts at a random port, which is annoying.
opencpu$start(8000)
browseURL("http://localhost:8000/ocpu/library/ICoVeR/www/", browser = getOption("browser"), encodeIfNeeded = FALSE)
This diff is collapsed.
This diff is collapsed.
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment