#' @title Running Star two steps for variant calls
#' @description This function executes the two steps STAR as sugested by best practice GATK for calling variants on RNAseq data only PE data are accepted
#'
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param fastq.folder, a character string indicating where gzip fastq files are 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 indexed reference genome for STAR is located.
#' @param groupid, a character string to be inserted in the bam as identifier for the sample
#' @param threads, a number indicating the number of cores to be used from the application
#' @param opossum.preprocessing, a boolean TRUE or FALSE to use opossum for RNAseq data preprocessing https://wellcomeopenresearch.org/articles/2-6/v1
#' @author Raffaele Calogero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy
#'
#' @return three files: dedup_reads.bam, which is sorted and duplicates marked bam file, dedup_reads.bai, which is the index of the dedup_reads.bam, and dedup_reads.stats, which provides mapping statistics
#' @examples
#'\dontrun{
#' #downloading fastq files
#' system("wget http://130.192.119.59/public/test_R1.fastq.gz")
#' system("wget http://130.192.119.59/public/test_R2.fastq.gz")
#' #running star2step nostrand pe
#' star2steps(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch",
#' genome.folder="/data/scratch/hg38star", groupid="test", threads=8, opossum.preprocessing=FALSE)
#'
#' }
#' @export
star2steps <- function(group=c("sudo","docker"),fastq.folder=getwd(), scratch.folder="/data/scratch", genome.folder, groupid, threads=1, opossum.preprocessing=FALSE){
home <- getwd()
setwd(fastq.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#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)
}
tmp.folder <- gsub(":","-",gsub(" ","-",date()))
scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
writeLines(scrat_tmp.folder,paste(fastq.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=fastq.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 ",scratch.folder,"/run.info ", scratch.folder,"/",tmp.folder,"/run.info", sep=""))
}
dir <- dir[grep(".fastq.gz$", dir)]
dir.trim <- dir[grep("trimmed", dir)]
cat("\ncopying \n")
if(length(dir)==0){
cat(paste("It seems that in ", fastq.folder, "there are not fastq.gz files"))
system("echo 1 > ExitStatusFile 2>&1")
setwd(home)
return(1)
}else if(length(dir.trim)>0){
dir <- dir.trim
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
for(i in dir){
system(paste("cp ",fastq.folder,"/",i, " ",scratch.folder,"/",tmp.folder,"/",i, sep=""))
}
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
}else if(length(dir)>2){
cat(paste("It seems that in ", fastq.folder, "there are more than two fastq.gz files"))
system("echo 2 > ExitStatusFile 2>&1")
setwd(home)
return(2)
}else{
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
for(i in dir){
system(paste("cp ",fastq.folder,"/",i, " ",scratch.folder,"/",tmp.folder,"/",i, sep=""))
}
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
}
#Trimmed fastq linking fpr docker
docker_fastq.folder=file.path("/data/scratch", tmp.folder)
#Trimmed fastq linking fpr docker
fastq <- sub(".gz$", "", dir)
cat("\nsetting as working dir the scratch folder and running docker container\n")
if(group=="sudo"){
# system("sudo docker pull docker.io/repbioinfo/star251.2017.01")
if(opossum.preprocessing){
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/repbioinfo/star251.2017.01 sh /bin/2step_star_opossum.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep="")
resultRun <- runDocker(group="sudo", params=params)
# system(paste("sudo docker run --privileged=true -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/rcaloger/star25.1 sh /bin/2step_star_opossum.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep=""))
}else{
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/repbioinfo/star251.2017.01 sh /bin/2step_star.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep="")
resultRun <- runDocker(group="docker", params=params)
# system(paste("sudo docker run --privileged=true -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/rcaloger/star25.1 sh /bin/2step_star.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep=""))
}
}else{
# system("docker pull docker.io/repbioinfo/star251.2017.01")
if(opossum.preprocessing){
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",docker_fastq.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/repbioinfo/star251.2017.01 sh /bin/2step_star_opossum.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep="")
resultRun <- runDocker(group="sudo", params=params)
# system(paste("docker run --privileged=true -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/rcaloger/star25.1 sh /bin/2step_star_opossum.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep=""))
}else{
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/repbioinfo/star251.2017.01 sh /bin/2step_star.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep="")
resultRun <- runDocker(group="docker", params=params)
# system(paste("docker run --privileged=true -v ",scratch.folder,":/data/scratch -v ",genome.folder,":/data/genome -d docker.io/rcaloger/star25.1 sh /bin/2step_star.sh ",docker_fastq.folder," ", threads," ", fastq[1]," ", fastq[2]," /data/genome ", groupid, " ", fastq.folder, sep=""))
}
}
if(resultRun==0){
out <- "out.info"
#system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
con <- file(paste(file.path(scratch.folder, tmp.folder),"out.info", sep="/"), "r")
tmp <- readLines(con)
close(con)
for(i in tmp){
i <- sub("mv ",paste("mv ",file.path(scratch.folder, tmp.folder),"/",sep=""),i)
system(i)
}
#running time 2
ptm <- proc.time() - ptm
con <- file(paste(fastq.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(fastq.folder,"run.info", sep="/"))
#running time 2
#removing temporary folder
#saving log and removing docker container
container.id <- readLines(paste(fastq.folder,"/dockerID", sep=""), warn = FALSE)
# system(paste("docker logs ", container.id, " >& ", substr(container.id,1,12),".log", sep=""))
system(paste("docker logs ", container.id, " >& ","star2steps_",substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
cat("\n\nRemoving the rsemStar temporary file ....\n")
system(paste("rm -R ",scrat_tmp.folder))
system(paste("rm -f ",fastq.folder,"/dockerID", sep=""))
system(paste("rm -f ",fastq.folder,"/tempFolderID", sep=""))
}
setwd(home)
}
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