run_gemma: 'Run serial gemma jobs on slurm-based HPC'

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

Description

Gemma Zhou lab: http://www.xzlab.org/software.html

Usage

run_gemma(inputdf, cmdno = 1, workdir = "largedata/",
  shid = "slurm-script/run_gemma_array.sh", email = NULL,
  runinfo = c(FALSE, "batch", "1", "2G", "1:00:00"))

Arguments

inputdf	An input data.frame for this function, including all the necessary pheno, geno file pathes, and other parameters. [data.frame, [df, cols=bfile, trait, kin, output]]
cmdno	Number of commands per CPU, i.e. number of rows per inputdf. [num, default=1].
workdir	The dir that will be cd to. [chr, default="largedata/"].
shid	The shell ID for this job. [chr, default is "slurm-script/run_gensel_array.sh"].
email	Your email address that farm will email to once the jobs were done/failed. [chr, default is NULL]
runinfo	Parameters specify the array job partition information. A vector of c(FALSE, "batch", "1", "2G", "8:00:00"): 1) run or not, default=FALSE 2) -p partition name, default=batch, 3) –ntasks=3, 4) –mem=30G, and 5) –time=8:00:00.

Value

return a batch of shell scripts.

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