check.R

#check if installation is correct

if(!file.exists(file.path(script.basename,"config.txt"))) {
  
  if (tryCatch(system("perl -e \"print 'hallo'\"",intern = T), error="nope") =="nope" ) stop("Failed to run perl. Please make sure that the command perl is available in your environment.")
  cat("No configuration file found.\n")
  cat("Please create a file config.txt in the home directory of the PrimerDesign tool.\n")
  cat("The first line of the file should specify the path to the binaries folder of NCBI blast (e.g. /home/User/ncbi-blast-2.6.0/bin)\n")
  cat("The second line of the file should specify the path to the folder containing the primer3_core executable (e.g. /home/User/primer3/). This folder also needs to contain a subfolder named primer3_config; this should usually be the case.\n")
  cat("The third line of the file should specify the path to the cliquer executable (e.g. /home/User/cliqr/cl)\n")
  cat("Primer3 and the config folder can be downloaded from https://github.com/primer3-org/primer3\n")
  cat("BLAST can be downloaded from https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download\n")
  stop("missing config.txt")
  # cat("This may be this first time you run PrimerDesign.\n")
  # cat("Please secify the path to the binaries folder of NCBI blast (e.g. /home/User/ncbi-blast-2.6.0/bin)\n")
  # cat("BLAST can be downloaded from https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download\n")
  # NCBI_path <- readLines(n=1)
  # if(!file.exists(file.path(NCBI_path, "makeblastdb"))) stop("No file named makeblastdb in",NCBI_path,"\nPlease specify a correct path to NCBI blast binaries")
  # 
  # cat("Please secify the path to the folder containing the primer3_core executable (e.g. /home/User/primer3/)\n")
  # cat("Folder also needs to contain a subfolder named primer3_config; this should usually be the case.\n")
  # cat("Primer3 and the config folder can be downloaded from https://github.com/primer3-org/primer3\n")
  # primer3_path <- readLines(n=1)
  # if(!file.exists(file.path(primer3_path, "primer3_core"))) stop("No file named primer3_core in", primer3_path,"\nPlease specify a correct path to primer3 binary")
  # if(!file.exists(file.path(primer3_path,"primer3_config/"))) stop("Error - please make sure that the primer3 path contains a folder primer3_config. If for some reason this is not the case, download the folder from https://github.com/primer3-org/primer3/tree/master/src")
  # 
  # writeLines(c(NCBI_path,primer3_path), con = file.path(script.basename,"config.txt"))
  # 
  
  
} else {
  NCBI_path <- readLines(file.path(script.basename,"config.txt"))[1]
  primer3_path <- readLines(file.path(script.basename,"config.txt"))[2]
  cliqr_path <- readLines(file.path(script.basename,"config.txt"))[3]
  if(!file.exists(file.path(NCBI_path, "makeblastdb")) | !file.exists(file.path(primer3_path, "primer3_core"))) {
    file.remove(file.path(script.basename,"config.txt"))
    stop("The config.txt file was incorrect. I have removed the file, please restart the program and specify correct paths to NCBI Blast and primer3.")
  }
  
}

pkgTest <- function(x, bc =F) {
    print(paste0('Testing for R package: ',x,' ...'))
    if (!require(x,character.only = TRUE))
    {
        cat("Package",x,"is missing, installing...")
        if (bc){
            if(getRversion() >= 3.5){
                BiocManager::install(x)
            }else{
                biocLite(x)
            }
        }else{
            install.packages(x,dep=TRUE,repos = "http://cran.us.r-project.org")
        }
        if(!require(x,character.only = TRUE)) stop("Package not found")
    }
}

if(getRversion() >= 3.5){
    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager",repos = "http://cran.us.r-project.org")
}else{
    source("https://bioconductor.org/biocLite.R")
}

pkgTest("getopt")
pkgTest("R.utils")
pkgTest("utils")
pkgTest("magrittr")
pkgTest("stringr")
pkgTest("igraph")
pkgTest("GenomicRanges", bc=T) #bionductor
pkgTest("rtracklayer", bc=T) #bioconductor
pkgTest("GenomicFeatures", bc=T) #bioconductor