getQsubargs {systemPipeR} | R Documentation |
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
.
getQsubargs(software = "qsub", queue = "batch", Nnodes = "nodes=1", cores = as.numeric(gsub("^.* ", "", tophatargs$args["p"])), memory = "mem=10gb", time = "walltime=20:00:00")
software |
Software to use for submission to queuing system. Default is |
queue |
Name of queue to to use. Default is |
Nnodes |
Number of compute nodes to use for processing. Default is |
cores |
Number of CPU cores to use per compute node. Default will use what is provided by under |
memory |
Amount of RAM to reserve per node. |
time |
Walltime limit each job is allowed to run per node. |
list
Thomas Girke
## Construct SYSargs object from param and targets files param <- system.file("extdata", "tophat.param", package="systemPipeR") targets <- system.file("extdata", "targets.txt", package="systemPipeR") args <- systemArgs(sysma=param, mytargets=targets) args names(args); modules(args); cores(args); outpaths(args); sysargs(args) ## Not run: ## Execute SYSargs on single machine runCommandline(args=args) ## Execute SYSargs on multiple machines qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00") qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR") ## Alignment stats read_statsDF <- alignStats(fqpaths=tophatargs$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)