Table of contents
Install HaplotypR
To install HaplotypR start R and first install ShortRead by typing:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ShortRead")
Then install devtools by typing
install.packages("devtools")
install.packages("git2r")
and install Rswarm, Rvsearch and HaplotypR by typing
library(devtools)
library(git2r)
path <- file.path(tempfile(pattern="Rswarm-"), "Rswarm")
dir.create(path, recursive=TRUE)
repo <- clone("https://github.com/lerch-a/Rswarm.git", path)
clone("https://github.com/torognes/swarm.git", file.path(path, "src", "swarm"))
install(path)
path <- file.path(tempfile(pattern="Rvsearch-"), "Rvsearch")
dir.create(path, recursive=TRUE)
repo <- clone("https://github.com/lerch-a/Rvsearch.git", path)
clone("https://github.com/torognes/vsearch.git", file.path(path, "src", "vsearch"))
install(path)
detach("package:HaplotypR", unload=TRUE)
devtools::install_gith
Run HaplotypR on R command line
Workflow:
Run HaplotypR as Shiny App (currently dysfunctional)
Load HaplotypR package:
library("HaplotypR")
Copy Example Files to a working directory ‘outputDir’:
# Define output directory
outputDir <- "~/exampleHaplotypR"
# Create output directoy
if(!dir.exists(outputDir))
dir.create(outputDir, recursive=T)
# Set working directory to output directory
setwd(outputDir)
# Copy example files to output directory
file.copy(from=system.file(package="HaplotypR", "extdata"), to=outputDir, recursive = T)
# List files example files in output directory
dir(file.path(outputDir, "extdata"))
The listed file can be used as example input files in the shiny app. The following files should be listed with the last R command: “barcode_Fwd.fasta”, “barcode_Rev.fasta”, “markerFile.txt”, “readsF.fastq.gz”, “readsR.fastq.gz”, “sampleFile.txt”.
Run HaplotypR GUI:
install.packages("shiny")
install.packages("shinyFiles")
runShinyApp()