#' @title A function to create a genome index for indrop V2 single cell data
#' @description This function executes a docker that produces as output the genome index index for bowtie
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param index.folder, a character string indicating the folder where the index will be created. The index will have the prefix genome.
#' @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
#' @author Raffaele Calogero and Riccardo Panero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy
#'
#' @examples
#' \dontrun{
#' library(rCASC)
#' #running indropCounts index build
#' indropIndex(group="docker", index.folder=getwd(),
#' ensembl.urlgenome="ftp://ftp.ensembl.org/pub/release-87/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz",
#' ensembl.urlgtf="ftp://ftp.ensembl.org/pub/release-87/gtf/mus_musculus/Mus_musculus.GRCm38.87.gtf.gz")
#' }
#'
#' @export
indropIndex <- function(group=c("sudo","docker"), index.folder, ensembl.urlgenome, ensembl.urlgtf){
#testing if docker is running
test <- dockerTest()
if(!test){
cat("\nERROR: Docker seems not to be installed in your system\n")
return()
}
#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(index.folder)){
cat(paste("\nIt seems that the ",index.folder, " folder does not exist\n"))
return(2)
}
setwd(index.folder)
yaml.file=paste(path.package(package="rCASC"),"extras/indrop.yaml",sep="/")
system(paste("cp ",yaml.file," ", file.path(index.folder),sep=""))
system(paste("chmod 777 -R", file.path(index.folder)))
#edit yaml
yaml <- readLines("indrop.yaml")
project_name <- yaml[grep("project_name", yaml)]
project_name <- sub("CRISPR", "INDEX", project_name)
yaml[grep("project_name", yaml)] <- project_name
# project_dir <- yaml[grep("project_dir", yaml)]
# project_dir <- sub("/sto2/labcamargo/Documents/single_cell/CRISPR_single_cell_9Nov17/inDrops/", "/data/scratch", project_dir)
# yaml[grep("project_dir", yaml)] <- project_dir
# sample_name <- yaml[grep(" - name :", yaml)]
# sample_name <- sub("CRISPR", sample.name, sample_name)
# yaml[grep(" - name :", yaml)] <- sample_name
# input_dir <- yaml[grep(" dir :", yaml)]
# input_dir <- sub("/sto2/labcamargo/Documents/single_cell/CRISPR_single_cell_9Nov17/basespace/171004_M00620_0217_000000000-BFWPC_FASTQ", "/data/scratch/input", input_dir)
# yaml[grep(" dir :", yaml)] <- input_dir
# split_affixes <- yaml[grep(" split_affixes :", yaml)]
# split_affixes <- sub("S1_L001", split.affixes, split_affixes)
# yaml[grep(" split_affixes :", yaml)] <- split_affixes
# library_name <- yaml[grep("library_name:", yaml)]
# library_name <- gsub("Sample1", sample.name, library_name)
# yaml[grep("library_name:", yaml)] <- library_name
bowtie_index <- yaml[grep("bowtie_index :", yaml)]
bowtie_index <- gsub("/sto2/labcamargo/Documents/bowtie_index/mm10/Mus_musculus.GRCm38.85.index", "/index/genome", bowtie_index)
yaml[grep("bowtie_index :", yaml)] <- bowtie_index
#UMI parameters
# m <- yaml[grep(" m : 10 #Ignore reads with more than M alignments, after filtering on distance from transcript end.", yaml)]
# m <- sub("10", M, m)
# yaml[grep(" m : 10 #Ignore reads with more than M alignments, after filtering on distance from transcript end.", yaml)] <- m
# u <- yaml[grep(" u : 2 #Ignore counts from UMI that should be split among more than U genes.", yaml)]
# u <- sub("2", U, u)
# yaml[grep(" u : 2 #Ignore counts from UMI that should be split among more than U genes.", yaml)] <- u
# d <- yaml[grep(" d : 400 #Maximal distance from transcript end, NOT INCLUDING THE POLYA TAIL", yaml)]
# d <- sub("400", D, d)
# yaml[grep(" d : 400 #Maximal distance from transcript end, NOT INCLUDING THE POLYA TAIL", yaml)] <- d
#outout params
# low_complexity_mask <- yaml[grep(" low_complexity_mask: False", yaml)]
# low_complexity_mask <- sub("False", low.complexity.mask, low_complexity_mask)
# yaml[grep(" low_complexity_mask: False", yaml)] <- low_complexity_mask
zz <- file("indrop.yaml", "w")
writeLines(yaml, zz)
close(zz)
#
system(paste("chmod 777 -R", file.path(index.folder)))
params <- paste("--cidfile ",index.folder,"/dockerID -v ", index.folder,":/index -d docker.io/repbioinfo/indrop.2017.01 sh /bin/indropIndex.sh ", ensembl.urlgenome, " ", ensembl.urlgtf, sep="")
resultRun <- runDocker(group=group, params=params)
# if(group=="sudo"){
# params <- paste("--cidfile ",index.folder,"/dockerID -v ", index.folder,":/index -d docker.io/repbioinfo/indrop.2017.01 sh /bin/indropIndex.sh ", ensembl.urlgenome, " ", ensembl.urlgtf, sep="")
# resultRun <- runDocker(group="sudo",container="docker.io/repbioinfo/indrop.2017.01", params=params)
# }else{
# params <- paste("--cidfile ",index.folder,"/dockerID -v ", index.folder,":/index -d docker.io/repbioinfo/indrop.2017.01 sh /bin/indropIndex.sh ", ensembl.urlgenome, " ", ensembl.urlgtf, sep="")
# resultRun <- runDocker(group="docker",container="docker.io/repbioinfo/indrop.2017.01", params=params)
# }
if(resultRun==0){
cat("\n inDrop genome index generation is finished\n")
}
#running time 2
ptm <- proc.time() - ptm
dir <- dir(index.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("inDrop index user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("inDrop index system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("inDrop index elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("inDrop index user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("inDrop index system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("inDrop index elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
#saving log and removing docker container
container.id <- readLines(paste(index.folder,"/dockerID", sep=""), warn = FALSE)
system(paste("docker logs ", substr(container.id,1,12), " &> ",index.folder,"/indropIndex_", 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="/")," ",index.folder, sep=""))
setwd(home)
}
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