#' @title Download for the first time all containers embedded in the workflows
#' @description This is a functin that preapre the docker environment to be used for the first time the docker4seq is installed.
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param containers.file, a character string with the name of the file which indicate which are the initial set of containers to be downloaded. Initally the set is given by a file located in the folder containers of docker4seq package: "all", "rnaseq", "ncrnaseq", "chipseq"
#' @author Raffaele Calogero
#'
#' @examples
#'\dontrun{
##' #running runDocker
#' downloadContainers(group="docker", containers.file)
#'
#' }
#' @export
downloadContainers <- function(group="docker", containers.file="all"){
if(containers.file=="all"){
containers.file=paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")
}else if(containers.file=="rnaseq"){
containers.file=paste(path.package(package="docker4seq"),"containers/rnaseq.txt",sep="/")
}else if(containers.file=="ncrna"){
containers.file=paste(path.package(package="docker4seq"),"containers/ncrna.txt",sep="/")
}else if(containers.file=="chipseq"){
containers.file=paste(path.package(package="docker4seq"),"containers/chipseq.txt",sep="/")
}
containers <- readLines(containers.file)
for(i in containers){
if(group=="sudo"){
system(paste("sudo docker pull ",i, sep=""))
}else if(group=="docker"){
system(paste("docker pull ",i, sep=""))
}else{
cat("\nThe group provides is neither sudo or docker\n")
return(2)
}
}
writeLines(containers, paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/"))
}
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