bsub_cmd: bsub_cmd

In mskilab/skitools: Various mskilab R utilties

bsub_cmd

Description

Makes bsub command that wraps shell command "cmd" to send to queue "queue" redirebmccting output / error etc streams to path prefixed by "jname", optional_args: maximum memory requirements "mem", "jlabel" job label b

Usage

bsub_cmd(
  cmd,
  queue,
  jname = NULL,
  jlabel = NULL,
  jgroup = NULL,
  mem = NULL,
  group = "cgafolk",
  cwd = NULL,
  mc.cores = NULL,
  deadline = F
)

Arguments

cmd	length n vector of shell commands, optionally named, one per job
queue	optional length n or length 1 character specifying queue to send jobs to (default hour)
jname	optional length n character specifying names of jobs, this will be the root of the output files generated by the job
jlabel	optional length n character specifying labels of jobs, this the string
jgroup	optional length n character specifying job group name
mem	length n or length 1 integer specifying GB of memory to be used by jobs
group	character specifying job group (default cgafolk)
cwd	character specifying which working directory to launch jobs from (default is current working directory of R session)
mc.cores	length n or 1 integer specifying how many cores to assign to each job
deadline	logical flag whether to send jobs to deadline queue

Value

character vector of bsub commands, which can run using system or dumped to a shell script

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.