Description Usage Arguments Value Examples
Farm is a computer cluster running slurm system. Note, bigmem mem=8000 per cpu, hi med low mem=25000 per cpu, serial mem=1500 per cpu.
1 2 3 4 5 | set_array_job(shid = "largedata/GenSel/CL_test.sh",
shcode = "sh largedata/myscript.sh", arrayjobs = "1-700", wd = NULL,
jobid = "myjob", email = NULL, runinfo = c(TRUE, "bigmemh", "1"))
get_runinfo(runinfo)
|
shid |
Relative or absolute path and file name of your shell code, i.e. CL_test.sh. |
shcode |
The commands inside your sh file. |
arrayjobs |
A character specify the number of array you try to run, i.e. 1-100. |
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 or failed. |
runinfo |
Parameters specify the array job partition information. A vector of c(TRUE, "bigmemh", "1"): 1) run or not, 2) -p partition name, and 3) –cpus. |
return a shell file.
1 2 3 4 5 6 7 8 9 10 | for(i in 1:10){
shid <- paste0("slurm-script/run_", i, ".sh")
command <- paste0("bedtools getfasta -name -tab -fi roast.chrom.", i, ".msa.in")
cat(command, file=shid, sep="\n", append=FALSE)
}
shcode <- paste("module load bismark/0.14.3", "sh slurm-script/run_$SLURM_ARRAY_TASK_ID.sh", sep="\n")
set_array_job(shid="slurm-script/run.sh", shcode=shcode,
arrayjobs="1-10", wd=NULL, jobid="myjob", email=NULL,
run = c(TRUE, "bigmemh", "8196", "1"))
|
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