subScript: subScript will submit a script to the cluster
In PietaSchofield/pietalib: A Small Collection Of Useful Functions

Description Usage Arguments

calls subJob to submit a script to the cluster as a temporary file it relies on the temporary directory where the temporary file will be written to being mounted to the local machine. I could get round this by writing it locally and then copying it with scp but at the moment this is not worth the effort.

subScript(scriptstub = "pieta_qsub", script = c("#!/bin/bash", "hostname"),
  scriptext = ".sh", tmpdir = "/homes/pschofield/tmp/", logdir = "",
  cores = 8, nosub = FALSE, email = "as", queue = NULL,
  emailAddress = "p.schofield@dundee.ac.uk", args = NULL, ramSize = "4G",
  nNodes = 1)

`scriptstub`	the stub for the temporary file name
`script`	the content of the script as a vector of strings
`scriptext`	extention for the temporary file
`tmpdir`	location for the temporary file
`logdir`	location for the batch job logs
`cores`	number of cores
`nosub`	boolean to switch off actual submission but to create the tempfiles
`email`	job status email settings
`queue`	queue name
`emailAddress`	where to send job status emails
`args`	any arguments to add to the job submission string