getQsubargs: Arguments for qsub

In systemPipeR: systemPipeR: NGS workflow and report generation environment

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

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  
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")

## End(Not run)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.