run_Rcodes: 'Run array job of R codes'

In yangjl/farmeR: Generate pipelines for maize Genomic and Genetic analysis

Description

Run array job of R codes

Usage

run_Rcodes(inputdf, outdir, cmdno = 100, rcodes = "lib/C_format.R",
  arrayshid = "slurm-script/run_bcf_query_array.sh", email = NULL,
  runinfo = c(FALSE, "bigmemh", 1))

Arguments

inputdf	An input data.frame, with columns of file and out.
outdir	The dir of shell files.
cmdno	Number of commands to excute in each array.
rcodes	The abosulte path of your R codes to run.
arrayshid	The sbatch id.
email	Your email address that farm will email to once the jobs were done/failed.
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "bigmemh", "1"): 1) run or not, default=FALSE 2) -p partition name, default=bigmemh and 3) –cpus, default=1. It will pass to set_array_job.
cmdno	Number of commands per CPU, i.e. number of rows per inputdf.

Value

return a batch of shell scripts.

Examples

run_Rcodes(inputdf=data.frame(file=1:11, out=10), outdir="slurm-script", cmdno=10,
           rcodes = "lib/C_format.R", arrayshid = "slurm-script/run_rcode_array.sh",
           email=NULL, runinfo = c(FALSE, "bigmemh", 1))

yangjl/farmeR documentation built on May 4, 2019, 2:28 p.m.