| runCommandline {systemPipeR} | R Documentation |
Function to execute system parameters specified in SYSargs object
runCommandline(args, runid = "01", make_bam=TRUE, ...)
args |
object of class |
runid |
Run identifier used for log file to track system call commands. Default is |
make_bam |
Autodetects SAM file outputs and converts them to sorted and indexed BAM files. Default is |
... |
Additional arguments to pass on to |
Output files, their paths can be obtained with outpaths() from SYSargs container.
In addition, a character vector is returned containing the same paths.
Thomas Girke
## 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)