bash_job: bash job using conda env

In leylabmpi/LeyLabRMisc: Ley Lab misc R functions, rmd templates, etc.

bash job using conda env

Description

The conda setup is assumed to be in your ~/.bashrc If print_output == TRUE: the stdout/stderr will be printed instead of returned Else: the stdout/stderr with be returned by the function stderr/stdout is printed unless print_output==FALSE

Usage

bash_job(
  cmd,
  conda_env = NULL,
  stdout = TRUE,
  stderr = TRUE,
  print_output = TRUE,
  return_output = FALSE,
  log_file = NULL,
  verbose = TRUE,
  wait = TRUE
)

Arguments

cmd	The bash command in a string format
conda_env	The conda env to use
stdout	If TRUE, print the stdout; if file path, write to file
stderr	If TRUE, print the stderr; if file path, write to file
print_output	Pretty printing of the output to the console?
return_output	Return the bash command output?
verbose	Write status messages?
wait	Wait for the process to finish?

Examples

# simple
bash_job('ls -thlc')
# write stderr to log file
bash_job('ls -thlc', stderr='log.txt')
# use conda environment
bash_job('conda list', conda_env='base')
# return output
files = bash_job('find . -name \\"*ipynb\\"', return_output=TRUE, print_output=FALSE, verbose=FALSE)

leylabmpi/LeyLabRMisc documentation built on June 13, 2025, 9:29 a.m.