getSubCmdTokens,ClusterArchitectureSLURM-method {RnBeads} | R Documentation

## getSubCmdTokens-methods

### 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")

[Package RnBeads version 2.2.0 Index]