systemPipeR (version 1.6.2)

runCommandline: Execute SYSargs

Description

Function to execute system parameters specified in SYSargs object

Usage

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

Arguments

args

object of class SYSargs

runid

Run identifier used for log file to track system call commands. Default is "01".

...

Additional plotting 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.

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)

## 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")