#' @title A function to handle fasterq-dumper SRA to download SRA fastq files
#' @description This function executes a ubuntu docker that produces as output FASTQCstdin_fastqc.html and stdin_fastqc.zip files
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param sra.name, a character string indicating the name of the SRA object to be download
#' @param data.folder, a character string indicating the working folder where output folder will be written
#' @param scratch.folder, a character string indicating the temporary folder for data preprocessing
#' @param threads, a integer indicating the number of threads to be used from fasterq-dumper
#' @author Raffaele Calogero, raffaele.calogero [at] unito [dot] it, University of Torino
#'
#' @examples
#' \dontrun{
#' #running sraDownload
#' sraDownload(group="docker", sra.name="SRR7762358", data.folder=getwd(), scratch.folder="/data/scratch", threads=8)
#' system("mv ./SRR7762358/SRR7762358.fastq.gz ./SRR7762358/SRR7762358_S1_L001_R1_001.fastq.gz")
#' }
#'
#' @export
sraDownload <- function(group=c("sudo","docker"), sra.name, data.folder, scratch.folder, threads=8){
#storing the position of the home folder
home <- getwd()
#running time 1
ptm <- proc.time()
#setting the data.folder as working folder
if (!file.exists(data.folder)){
cat(paste("\nIt seems that the ",data.folder, " folder does not exist\n"))
return(2)
}
setwd(data.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#testing if docker is running
test <- dockerTest()
if(!test){
cat("\nERROR: Docker seems not to be installed in your system\n")
system("echo 10 > ExitStatusFile 2>&1")
setwd(home)
return(10)
}
#executing the docker job
params <- paste("--cidfile ",data.folder,"/dockerID -v ",data.folder, ":/workingdir -v ", scratch.folder, ":/tmpfolder -d docker.io/repbioinfo/sra.2018.01 bash /bin/sra.download.sh ", sra.name, " ", threads, sep="")
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
cat("\nsra fasterq dump is finished\n")
}
#running time 2
ptm <- proc.time() - ptm
dir <- dir(data.folder)
dir <- dir[grep("run.info",dir)]
if(length(dir)>0){
con <- file("run.info", "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("sra fasterq dump user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sra fasterq dump system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sra fasterq dump elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("sra fasterq dump user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sra fasterq dump system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("sra fasterq dump elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
#saving log and removing docker container
container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
system(paste("docker logs ", substr(container.id,1,12), " &> ",data.folder,"/sraDownload_", substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
cat("\n\nRemoving the temporary file ....\n")
system("rm -fR dockerID")
system(paste("cp ",paste(path.package(package="rCASC"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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