05.nrm.create.realized.birds.shellscript.R

# shellscripts to create realized distribution maps for birds

# define location of R scripts
script.dir = "/home/jc140298/NRM/dev"

# define working dir
wd = "/rdsi/ccimpacts/NRM"
pbs.dir = paste(wd, "/tmp.pbs", sep=""); setwd(pbs.dir)

# define taxa
taxon = "birds"; taxon.dir = paste(wd, "/", taxon, sep="")

# get a list of species directories
species.names = list.files(paste(taxon.dir, "/models", sep="")) #get a list of all the species

for (sp in species.names) { # cycle through each of the species

	# create the shell file
	shell.file.name = paste(pbs.dir, "/05.nrm.create.realized.birds.", sp, ".sh", sep="")
	
	shell.file = file(shell.file.name, "w")
		cat('#!/bin/bash\n', file=shell.file)
		cat('#PBS -j oe\n', file=shell.file) # combine stdout and stderr into one file
		cat('#PBS -l pmem=24gb\n', file=shell.file)
		cat('#PBS -l nodes=1:ppn=1\n', file=shell.file)
		cat('#PBS -l walltime=1:00:00\n', file=shell.file)
		cat('cd $PBS_O_WORKDIR\n', file=shell.file)
#		cat('#PBS -l epilogue=/home/jc140298/epilogue/epilogue.sh\n', file=shell.file)
		cat('module load R\n', file=shell.file) # need for R
		cat("R CMD BATCH --no-save --no-restore '--args wd=\"", wd, "\" taxon=\"", taxon, "\" sp=\"", sp, "\"' ", script.dir, "/05.nrm.create.realized.birds.R ", pbs.dir, "/05.nrm.create.realized.birds.", sp, ".Rout \n", sep="", file=shell.file)
	close(shell.file)
		
	# submit job
	system(paste("qsub ", shell.file.name, sep=""))
	Sys.sleep(5)
	
} # end for species