Process batches (DBAS) using SLURM by selecting directories

Choose which batches to process by selecting the directory where the measurement files are stored. `dbaScreeningSelectedBatchesSlurm()` will create necessary files for submission of the job to the workflow manager SLURM.

Usage

dbaScreeningSelectedBatchesSlurm(
  msrawfileIndex,
  batchDirs,
  saveDirectory,
  email
)

Arguments

msrawfileIndex

Name of index where processing information is stored

batchDirs

Directory of measurement files (recursive, multiple permitted)

saveDirectory

Location where SLURM job files should be saved

email

Address for SLURM notifications

Details

Three files are created, the records of all files to process, organized into batches (.RDS); the R script which SLURM needs to run, and the SLURM job file (.sbatch). The command needed to start the process is given as a message (you may need to switch to a SLURM-enabled server).

Examples

if (FALSE) { # \dontrun{
userEmail <- "example@bafg.de"
dirResults <- "processingResults"
msrawfileIndexName <- "ntsp25.2_msrawfiles"
library(ntsportal)
connectNtsportal()
file.remove(list.files(dirResults, f = T))

dbaScreeningSelectedBatchesSlurm(
  msrawfileIndex = msrawfileIndexName,
  batchDirs = "/root/dir/all/msrawfiles",
  saveDirectory = dirResults,
  email = userEmail
)
} # }