bsub_cmd: bsub_cmd

View source: R/utils.R

bsub_cmdR Documentation

bsub_cmd

Description

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

Usage

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

Arguments

cmd

string shell command to be submitted via bsub

queue

string name of specified queue, '-q "queue_name" ' (default = NULL)

jname

string path prefix by 'jname' (default = NULL)

jlabel

string job name for '-J "job_name" ' (default = NULL)

jgroup

string job_group_name for '-g "job_group_name" ' (default = NULL)

mem

integer amount of virtual memory/RAM to use via resource requirement arg '-R "res_req"” (default = NULL)

group

string project_name for '-P' (default = NULL)

cwd

string pathname to current working directory; -cwd "current_working_directory" (default = NULL)

mc.cores

integer number of cores to use (default = 1)

deadline

boolean specifies if deadline initiation time used (default = FALSE)

Author(s)

Marcin Imielinski


mskilab/Flow documentation built on Jan. 12, 2023, 8:31 a.m.