set_farm_job: 'Set up one farm job'

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

Description

Farm is a computer cluster running slurm system. Note, bigmem mem=8000/cpu, hi/med/low mem=25000/cpu, serial mem=1500/cpu.

Usage

set_farm_job(slurmsh = "largedata/GenSel/CL_test.sh",
  shcode = "sh largedata/myscript.sh", wd = NULL, jobid = "myjob",
  email = NULL, runinfo = c(TRUE, "bigmemh", "1", "2G", "8:00:00"))

Arguments

slurmsh	Relative or absolute path and file name of your shell code, i.e. largedata/GenSel/CL_test.sh.
shcode	The commands inside your sh file.
wd	Working directory, default=NULL. It will use your current directory.
jobid	The job name show up in your sq NAME column.
email	Your email address that farm will email to once the job was done/failed.
runinfo	Parameters control the array job partition. c(TRUE, "bigmemh", "1", "2G", "8:00:00") A vector of c(TRUE, "bigmemh", "1"): 1) run or not, 2) -p partition name, 3) –ntasks.

Value

a shell file.

Examples

cmd <- paste0("snpconvert -a largedata/teo_updated/teo_raw_biallelic.hmp.txt",
" -i largedata/teo_updated/TeoCurated_20160308_AGPv2_flt_maf005m2.txt -s 12",
" -o largedata/teo_updated/teo_raw_biallelic_recoded_20160303_AGPv2.txt")

set_farm_job(slurmsh = "largedata/scripts/run_snpconvert.sh",
shcode = cmd, wd = NULL, jobid = "snpconvert", email=NULL, runinfo=c(TRUE, "bigmemh", "1"))

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