RnBeads (version 1.4.0)

getSubCmdTokens,ClusterArchitectureSGE-method: getSubCmdTokens-methods

Description

Returns a string for the of command line corresponding to submitting a job with the given command to the cluster.

Usage

"getSubCmdTokens"(object, cmd.tokens, log, job.name = "", res.req = character(0), depend.jobs = character(0), sub.binary = TRUE, quote.cmd = TRUE)

Arguments

object

ClusterArchitectureSGE object

cmd.tokens

a character vector specifying the executable command that should be wrapped in the cluster submission command

log

file name and path of the log file that the submitted job writes to

job.name

name of the submitted job

res.req

character vector specifying required resources. The resource requirements should be the values of the vector, the names should specify the resource name

depend.jobs

character vector containg names or ids of jobs the submitted job will depend on.

sub.binary

treat the command as binary (see -b flag of qsub of the SGE documentation)

quote.cmd

Flag indicating whether the submitted cammed should also be wrapped in quotes

Value

A character vector containing the submission command tokens

Details

For a concrete child class implementation for a sun grid architecture specification see ClusterArchitectureSGE

Examples

arch <- new("ClusterArchitectureSGE",
	name="my_sge_architecture"
)
getSubCmdTokens(arch,c("Rscript","my_great_script.R"),"my_logfile.log")