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Export jobs for external / array execution

Source: R/export_jobs.R
export_jobs.Rd

Writes a serialized job manifest plus a minimal, backend-agnostic run_one.R runner to dir. Deliberately emits no scheduler code: drive it with whatever array system you have, passing the 1-based job index as the first argument, e.g. Rscript run_one.R $SLURM_ARRAY_TASK_ID.

Usage

export_jobs(
  jobs,
  dir,
  overwrite = FALSE,
  setup = "library(fmrireg)",
  results_dir = "results"
)

Arguments

jobs

A single fmri_job or a list of them (e.g. from instantiate()).

dir

Output directory (created if needed).

overwrite

Overwrite an existing manifest. Default FALSE.

setup

Character vector of R lines run at the top of run_one.R before jobs are executed (load packages, set threads, etc.). Default loads fmrireg.

results_dir

Default output subdirectory written by run_one.R.

Value

Invisibly, a list describing what was written (dir, manifest, runner, n, ids).

See also

read_jobs(), run_jobs(), instantiate()

Examples

if (FALSE) { # \dontrun{
jobs <- instantiate(tmpl, manifest)
export_jobs(jobs, "study/jobs")
# then, per array task:  Rscript study/jobs/run_one.R $SLURM_ARRAY_TASK_ID
} # }