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]