runCommandline {systemPipeR} | R Documentation

## Execute SYSargs

### Description

Function to execute system parameters specified in `SYSargs` object

### Usage

    runCommandline(args, runid = "01", make_bam=TRUE, ...)

### Arguments

`args` | object of class `SYSargs`
`runid` | Run identifier used for log file to track system call commands. Default is `"01"`.
`make_bam` | Autodetects SAM file outputs and converts them to sorted and indexed BAM files. Default is `make_bam=TRUE`.
`...` | Additional arguments to pass on to `runCommandline()`.

### Value

Output files, their paths can be obtained with `outpaths()` from `SYSargs` container. In addition, a `character vector` is returned containing the same paths.

### 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 of a compute cluster
    resources <- list(walltime="00:25:00", nodes=paste0("1:ppn=", cores(args)), memory="2gb")
    reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.tmpl", Njobs=18, runid="01", resourceList=resources)

    ## Monitor progress of submitted jobs
    showStatus(reg)
    file.exists(outpaths(args))
    sapply(1:length(args), function(x) loadResult(reg, x)) # Works once all jobs have completed successfully.

    ## 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 1.16.1 Index]