getSubCmdTokens-ClusterArchitectureSGE-methods: getSubCmdTokens-methods

In RnBeads: RnBeads

Description

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

Usage

## S4 method for signature 'ClusterArchitectureSGE'
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

Details

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

Value

A character vector containing the submission command tokens

Author(s)

Fabian Mueller

Examples

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

RnBeads documentation built on March 3, 2021, 2 a.m.