bsub_cmd: bsub_cmd
In mskilab/Flow: Workflow and task management for genomics pipelines.

bsub_cmd

R 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)