bsub (version 1.1.0)

bsub_cmd: Submit shell commands

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 = ..., ...)
# }