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

Arguments

object	ClusterArchitectureSLURM 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	named vector of requested resources. Two options are available: "clock.limit" and "memory.size"
depend.jobs	character vector containg names or ids of jobs the submitted job will depend on.
sub.binary	flag indicating if the command is to be submitted using the "wrap" option of SLURM
quote.cmd	Flag indicating whether the submitted cammed should also be wrapped in quotes

Details

For a concrete child class implementation for a SLURM architecture specification see ClusterArchitectureSLURM

Value

A character vector containing the submission command tokens

Author(s)

Michael Scherer

Examples

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

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