getSubCmdTokens,ClusterArchitectureSGE-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 '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")

[Package RnBeads version 2.2.0 Index]