run_Rcode: 'Run array job of R codes'

In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description

Run array rcodes according to the parameters in the inputdf file. The array job number = nrow(inputdf).

Usage

run_Rcode(inputdf, outdir, cmdno = 1, rcodes = "lib/C_format.R",
  rversion = "3.5", base_shid = "run_bcf_query", email = NULL,
  runinfo = c(FALSE, "bigmemh", 5, "5G", "16:00:00", 1))

Arguments

inputdf	An input data.frame, with columns of file and out. [df, cols=file, out] Note, row parameter "j" will be passed to each array job!
outdir	The dir of shell files. [chr, "largedata/"]
cmdno	Number of commands to excute in each array. [num, =1]
rcodes	The abosulte path of your R codes to run. [chr, ="lib/C_format.R"]
rversion	R version used. [chr, ="3.5"]
base_shid	The base of the sbatch id. [chr, ="slurm-script/run_bcf_query"]
email	Your email address that farm will email to once the jobs were done/failed. [chr, =NULL]
runinfo	[vector, runinfo = c(FALSE, "bigmemh", 5, "5G", "16:00:00")]

Value

return a batch of shell scripts.

Examples

sh <- paste0('R --no-save --args ', j, ' < ', rcodes)
run_Rcode(inputdf=data.frame(file=1:11, out=10), outdir="slurm-script", cmdno=10,
           rcodes = "lib/C_format.R", arrayshid = "run_rcode",
           email=NULL, runinfo = c(FALSE, "bigmemh", 1))

yangjl/huskeR documentation built on Sept. 2, 2021, 5:38 a.m.