scripts/BatchJobs/makeClusterFunctionsAdaptive.R

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

makeClusterFunctionsAdaptive <- function (template.file)
{
  library(stringr)
  library(BatchJobs)
  template = cfReadBrewTemplate(template.file)
  submitJob = function(conf, reg, job.name, rscript, log.file,
                       job.dir, resources, arrayjobs) {
    outfile = cfBrewTemplate(conf, template, rscript, "pbs")
    res =  BatchJobs:::runOSCommandLinux("qsub", outfile, stop.on.exit.code = FALSE)
    max.jobs.msg = "Maximum number of jobs already in queue"
    output = paste0(res$output, collapse = "\n")
    if (grepl(max.jobs.msg, output, fixed = TRUE)) {
      makeSubmitJobResult(status = 1L, batch.job.id = NA_character_,
                          msg = max.jobs.msg)
    }
    else if (res$exit.code > 0L) {
      cfHandleUnknownSubmitError("qsub", res$exit.code,
                                 res$output)
    }
    else {
      makeSubmitJobResult(status = 0L, batch.job.id = str_extract(output,"\\d+"))
    }
  }
  killJob = function(conf, reg, batch.job.id) {
    cfKillBatchJob("canceljob", batch.job.id)
  }
  listJobs = function(conf, reg) {
    lj = BatchJobs:::runOSCommandLinux("qstat", "-u $USER")$output
    lj = grep("^([0-9]+).+", lj, value=TRUE)
    unique(as.numeric(gsub("^([0-9]+).*","\\1",lj)))
  }
  getArrayEnvirName = function() "PBS_ARRAYID"
  makeClusterFunctions(name = "Adaptive", submitJob = submitJob,
                       killJob = killJob, listJobs = listJobs, getArrayEnvirName = getArrayEnvirName)
}