#' \code{Run iget and iput to get/put data from/to iPlant.}
#'
#' Downloading SRA using 'ascp' utility or Aspera Connect.
#'
#' see more detail about SRA with Aspera downloading:
#' \url{http://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using}
#'
#' @param sra An input data.frame for SRA ids. Must contains column: SRR.
#' @param maxspeed The max speed for downloading.
#' @param outdir The output directory.
#' @param arrayjobs A character specify the number of array you try to run, i.e. 1-100.
#' @param jobid The job name show up in your sq NAME column.
#' @param email Your email address that farm will email to once the job was done/failed.
#'
#' @return return a batch of shell scripts.
#'
#' @examples
#'
#' @export
run_iput <- function(files, jobs1cpu=1,
localpwd="largedata/gatk_vcf",
email=NULL, runinfo = c(FALSE, "bigmemh", 1)){
####
for(j in 1:ceiling(length(files)/jobs1cpu)){
srow <- jobs1cpu*(j-1) + 1
erow <- jobs1cpu*j
cmd <- c()
for(k in srow:erow){
sh1 <- paste0("iput -X ", files[k])
cmd <- c(cmd, sh1)
}
shid <- paste0(localpwd, "/iput_", j, ".sh")
### header of the shell code
cat("### iput data from farm to iPlant",
paste("###", format(Sys.time(), "%a %b %d %X %Y")),
paste(""),
cmd,
file=shid, sep="\n", append=FALSE)
}
message("### run following:")
message("### for example: sh input_j.sh")
#shcode <- "sh slurm-script/iput_$SLURM_ARRAY_TASK_ID.sh"
#set_array_job(shid="slurm-script/run_iput_array.sh",
# shcode=shcode, arrayjobs=paste0("1-", ceiling(length(files)/jobs1cpu)),
# wd=NULL, jobid="iput", email=email, runinfo=runinfo)
# sbatch -p bigmemh --mem 32784 --ntasks=4 slurm-script/run_gatk_array.sh
}
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