Running structure in R in parallel

run_structure_fromR.R

library(parallel)
library(stringr)
# prelim setup
structure_binary <- "/path/to/structure"
n.cores <- 8

# number of Ks to try
tryK <- 1L:20L
n.runs <- 1L:20L

# output files (will be appended by out_f from structure)
out_files <- outer(n.runs, tryK, function(x,y) paste0("str_run_", str_pad(x, width = 2, pad = 0), "_K_", str_pad(y, width = 2, pad = 0), ".out")
log_files <- gsub("out", "log", out_files)

# create function to run structure, assumes that mainparams/extraparams file is in same path as current wd in Rscript
run_structure <- function(out_file, log_file) {
  k <- as.integer(str_extract(out_file, "[0-9]{2}\\b"))
  return(system(paste(structure_binary, "-K", k, "-o", out_file, "&>", log_file)))
}

mcmapply(run_structure, out_files, log_files, mc.cores = n.cores)