bsub_cmd {bsub} | R Documentation |
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 |
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_chunk
submits R code. -
bsub_script
submits R scripts.
Examples
## Not run:
bsub_cmd("samtools sort ...", name = ..., memory = ..., cores = ..., ...)
## End(Not run)
[Package bsub version 1.1.0 Index]