getQsubargs {systemPipeR} | R Documentation

## Arguments for qsub

### Description

Note: This function as been deprecated. Please use `clusterRun` instead. `getQsubargs` defines arguments to submit runX job(s) to queuing system (e.g. Torque) via `qsub`.

### Usage

    getQsubargs(software = "qsub", queue = "batch", Nnodes = "nodes=1", cores = as.numeric(gsub("^.* ", "", tophatargs$args["p"])), memory = "mem=10gb", time = "walltime=20:00:00")

### Arguments

`software` | Software to use for submission to queuing system. Default is `qsub`.
`queue` | Name of queue to to use. Default is `batch`.
`Nnodes` | Number of compute nodes to use for processing. Default is `nodes=1`.
`cores` | Number of CPU cores to use per compute node. Default will use what is provided by under `-p` in `myargs` of `systemArgs()` output.
`memory` | Amount of RAM to reserve per node.
`time` | Walltime limit each job is allowed to run per node.

### Value

`list`

### Author(s)

Thomas Girke

### Examples

    ## Construct SYSargs object from param and targets files
    param <- system.file("extdata", "tophat.param", package="systemPipeR")
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    args <- systemArgs(sysma=param, mytargets=targets)
    args
    names(args); modules(args); cores(args); outpaths(args); sysargs(args)

    ## Not run:
    ## Execute SYSargs on single machine
    runCommandline(args=args)

    ## Execute SYSargs on multiple machines
    qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00")
    qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR")
    ## Alignment stats
    read_statsDF <- alignStats(fqpaths=tophatargs$infile1, bampaths=bampaths, fqgz=TRUE)
    read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
    write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

    ## End(Not run)

[Package systemPipeR version 1.20.0 Index]