systemPipeR (version 1.6.2)

SYSargs-class: Class "SYSargs"

Description

S4 class container for storing parameters of command-line- or R-based software. SYSargs instances are constructed by the systemArgs function from two simple tablular files: a targets file and a param file. The latter is optional for workflow steps lacking command-line software. Typically, a SYSargs instance stores all sample-level inputs as well as the paths to the corresponding outputs generated by command-line- or R-based software generating sample-level output files. Each sample level input/outfile operation uses its own SYSargs instance. The outpaths of SYSargs usually define the sample inputs for the next SYSargs instance. This connectivity is achieved by writing the outpaths with the writeTargetsout function to a new targets file that serves as input to the next systemArgs call. By chaining several SYSargs steps together one can construct complex workflows involving many sample-level input/output file operations with any combinaton of command-line or R-based software.

Objects from the Class

Objects can be created by calls of the form new("SYSargs", ...).

See Also

systemArgs and runCommandline

Examples

showClass("SYSargs")
## 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); targetsin(args); targetsout(args); targetsheader(args); 
software(args); modules(args); cores(args); outpaths(args) 
sysargs(args); other(args); reference(args); results(args); infile1(args)
infile2(args); outfile1(args); SampleName(args)

## Return sample comparisons
readComp(args, format = "vector", delim = "-")

## The subsetting operator '[' allows to select specific samples
args[1:4]

## Execute SYSargs on single machine
runCommandline(args=args)

## Execute SYSargs on multiple machines  
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(args), memory="mem=10gb", time="walltime=20:00:00")
qsubRun(appfct="runCommandline(args=args)", appargs=args, qsubargs=qsubargs, Nqsubs=1, submitdir="results", package="systemPipeR")

## Write outpaths to new targets file for next SYSargs step
writeTargetsout(x=args, file="default")