#' @title Running indel relignment and quality recalibration on bam generated by bwa function NOT READY TO GO ON STABLE
#' @description This function executes the docker container snvPreprocessing. IMPORTANT: the working folder require the presence of GenomeAnalysisTK.tar.bz2 files
#'
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param bam.folder, a character string indicating where bam file generated by bwa is located
#' @param scratch.folder, a character string indicating the scratch folder where docker container will be mounted
#' @param genome.folder, a character string indicating the folder where the index reference genome for bwa is located
#' @param gatk.file, a character string for GenomeAnalysisTK-X.Y.tar.bz2, this file should be located in the bam.folder
#' @param threads, a number indicating the number of cores to be used by the application
#' @author Raffaele Calogero
#'
#' @return bam and bai after indel relignment and quality recalibration.
#' @examples
#'\dontrun{
#' #downloading examples 1 million reads of mcf7 exome mixed with 1 million of mouse derived by human exome capturing
#' system("wget http://130.192.119.59/public/hs1m_mm1m_R1.fastq.gz")
#' system("wget http://130.192.119.59/public/hs1m_mm1m_R2.fastq.gz")
#'
#' #required for bwa 61Gb At the present time this is required to run mutect1
#' system("wget http://130.192.119.59/public/hg19_exome.tar.gz")
#' #this genome index is prepared to be used for indel realignment and quality recalibration
#'
#' #running snvPreprocessing
#' snvPreprocessing(group="docker",bam.folder=getwd(),
#' scratch.folder="/data/scratch",
#' genome.folder="/data/scratch/hg19_exome",
#' threads=24, gatk.file="GenomeAnalysisTK-3.7.tar.bz2")
#'
#' }
#' @export
snvPreprocessing <- function(group=c("sudo","docker"), bam.folder=getwd(), scratch.folder="/data/scratch", genome.folder, threads=8, gatk.file){
home <- getwd()
setwd(bam.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#renaming gatk.file
system(paste("mv ",gatk.file, " GenomeAnalysisTK.tar.bz2", sep=""))
#running time 1
ptm <- proc.time()
#running time 1
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)
}
#########check scratch folder exist###########
if (!file.exists(scratch.folder)){
cat(paste("\nIt seems that the ",scratch.folder, "folder does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(home)
return(3)
}
#############################################
tmp.folder <- gsub(":","-",gsub(" ","-",date()))
scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
writeLines(scrat_tmp.folder,paste(bam.folder,"/tempFolderID", sep=""))
cat("\ncreating a folder in scratch folder\n")
dir.create(file.path(scratch.folder, tmp.folder))
dir.create(file.path(scratch.folder, tmp.folder,"/tmp"))
dir <- dir(path=bam.folder)
dir.info <- dir[which(dir=="run.info")]
if(length(dir.info)>0){
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",bam.folder,"/run.info ", scratch.folder,"/",tmp.folder,"/run.info", sep=""))
}
dir <- dir[grep("dedup_reads.bam", dir)]
cat("\ncopying \n")
if(length(dir)==0){
cat(paste("It seems that in ", bam.folder, "there is not a bam file files"))
system("echo 1 > ExitStatusFile 2>&1")
setwd(home)
return(1)
}else if(length(dir)>1){
cat(paste("It seems that in ", bam.folder, "there is more than one bam file"))
system("echo 2 > ExitStatusFile 2>&1")
setwd(home)
return(2)
}else if(length(dir)==1){
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",bam.folder,"/",dir[1], " ",scratch.folder,"/",tmp.folder,"/", sep=""))
system(paste("cp ",bam.folder,"/",sub("bam$","bai$", dir[1]), " ",scratch.folder,"/",tmp.folder,"/", sep=""))
system(paste("cp GenomeAnalysisTK.tar.bz2 ",scratch.folder,"/",tmp.folder,"/", sep=""))
}
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
#fastq linking fpr docker
docker_bam.folder=file.path("/data/scratch", tmp.folder)
cat("\nsetting as working dir the scratch folder and running xenome docker container\n")
params <- paste("--cidfile ",bam.folder,"/dockerID -v ",docker_bam.folder,":/data/scratch -v ",genome.folder,":/genome -d docker.io/repbioinfo/snvpre.2017.01 sh /bin/gatk.sh ", threads," ",bam.folder, sep="")
resultRun <- runDocker(group=group, params=params)
if(resultRun==0){
system(paste("cp ", scrat_tmp.folder, "/* ", bam.folder, sep=""))
}
#running time 2
ptm <- proc.time() - ptm
con <- file(paste(bam.folder,"run.info", sep="/"), "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,paste(bam.folder,"run.info", sep="/"))
#saving log and removing docker container
container.id <- readLines(paste(bam.folder,"/dockerID", sep=""), warn = FALSE)
# system(paste("docker logs ", container.id, " >& ", substr(container.id,1,12),".log", sep=""))
system(paste("docker logs ", container.id, " >& ","snvPreprocessing_",substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
#removing temporary folder
cat("\n\nRemoving the xenome temporary file ....\n")
system(paste("rm -R ",scrat_tmp.folder))
system(paste("rm -f ",bam.folder,"/dockerID", sep=""))
system(paste("rm -f ",bam.folder,"/tempFolderID", sep=""))
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",bam.folder, sep=""))
setwd(home)
}
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