bsub_cmd: Submit shell commands

In bsub: Submitter and Monitor of the 'LSF Cluster'

Description

Submit shell commands

Usage

bsub_cmd(cmd,
    name = NULL,
    hours = 1,
    memory = 1,
    cores = 1,
    temp_dir = bsub_opt$temp_dir,
    output_dir = bsub_opt$output_dir,
    dependency = NULL,
    enforce = bsub_opt$enforce,
    local = bsub_opt$local,
    sh_head = bsub_opt$sh_head,
    ...)

Arguments

cmd	A list of commands.
name	If name is not specified, an internal name calculated by digest is automatically assigned.
hours	Running time of the job.
memory	Memory usage of the job. It is measured in GB.
cores	Number of cores.
temp_dir	Path of temporary folder where the temporary R/bash scripts will be put.
output_dir	Path of output folder where the output/flag files will be put.
dependency	A vector of job IDs that current job depends on.
enforce	If a flag file for the job is found, whether to enforce to rerun the job.
local	Run job locally (not submitting to the LSF cluster)?
sh_head	Commands that are written as head of the sh script.
...	Command-line arguments can also be specified as name-value pairs.

Value

Job ID.

See Also

• bsub_chunksubmits R code.

• bsub_script submits R scripts.

Examples

## Not run: 
bsub_cmd("samtools sort ...", name = ..., memory = ..., cores = ..., ...)

## End(Not run)

bsub documentation built on July 1, 2021, 5:07 p.m.