systemPipeR (version 1.6.2)

getQsubargs: Arguments for qsub

Description

Note: This function as been deprecated. Please use clusterRun instead. getQsubargs defines arguments to submit runX job(s) to queuing system (e.g. Torque) via qsub.

Usage

getQsubargs(software = "qsub", queue = "batch", Nnodes = "nodes=1", cores = as.numeric(gsub("^.* ", "", tophatargs$args["p"])), memory = "mem=10gb", time = "walltime=20:00:00")

Arguments

software

Software to use for submission to queuing system. Default is qsub.

queue

Name of queue to to use. Default is batch.

Nnodes

Number of compute nodes to use for processing. Default is nodes=1.

cores

Number of CPU cores to use per compute node. Default will use what is provided by under -p in myargs of systemArgs() output.

memory

Amount of RAM to reserve per node.

time

Walltime limit each job is allowed to run per node.

Value

• list

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  
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00")
qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR")
## 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")