#' @title Generating bowtie2 genome index
#' @description This function executes the docker container bowtie2 where bowtie2-2.2.9 is installed. The index is created using ENSEMBL genome fasta file. User needs to provide the URL for ENSEMBL genome located in the ENSEMBL ftp
#'
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param genome.folder, a character string indicating the folder where the indexed reference genome for Bowtie will be located
#' @param ensembl.urlgenome, a character string indicating the URL from ENSEMBL ftp for the unmasked genome sequence of interest
#' @param ensembl.urlgtf, a character string indicating the URL from ENSEMBL ftp for the GTF for genome of interest
#' @param threads, a number indicating the number of cores to be used from the application
#' @author Raffaele Calogero
#'
#' @return The indexed Bowtie genome reference sequence
#' @examples
#'\dontrun{
#' #running rsemstar index for human
#' bowtie2Index(group="docker",genome.folder="/data/scratch/hg38bowtie2",
#' ensembl.urlgenome=
#' "ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz",
#' ensembl.urlgtf=
#' "ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh38.87.gtf.gz",
#' threads=8)
#'
#' }
#' @export
bowtie2Index <- function(group=c("sudo","docker"), genome.folder=getwd(), ensembl.urlgenome=NULL, ensembl.urlgtf=NULL, threads=1){
home <- getwd()
#########check scratch folder exist###########
if (!file.exists(genome.folder)){
cat(paste("\nIt seems that the ",genome.folder, "folder does not exist, I create it\n"))
dir.create(genome.folder)
}
#############################################
setwd(genome.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)
}
cat("\nsetting as working dir the genome folder and running bowtie2 docker container\n")
params <- paste("--cidfile ",genome.folder,"/dockerID -v ",genome.folder,":/genome"," -d repbioinfo/bowtie2.2018.01:bowtie2-2.2.9-R3.4.4-Bioconductor3.6-Biostrings_2.46.0 sh /bin/bowtie2.index.sh ",ensembl.urlgenome," ",ensembl.urlgtf," ",threads, sep="")
resultRun <- runDocker(group=group, params=params)
if(resultRun==0){
cat("\nBOWTIE2 index generation is finished\n")
}
#running time 2
ptm <- proc.time() - ptm
con <- file(paste(genome.folder,"run.info", sep="/"), "r")
tmp.run <- readLines(con)
close(con)
tmp.run <- NULL
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(genome.folder,"run.info", sep="/"))
#saving log and removing docker container
container.id <- readLines(paste(genome.folder,"/dockerID", sep=""), warn = FALSE)
system(paste("docker logs ", container.id, " >& ", "rsemstarIndex_",substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
#running time 2
system(paste("rm ",genome.folder,"/dockerID", sep=""))
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",genome.folder, sep=""))
setwd(home)
}
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