External shell commands for 'RAVE' — cmd-external • ravecore

These shell commands are only tested on 'MacOS' and 'Linux'. On 'Windows' machines, please use the 'WSL2' system. and 'CT'

Usage

cmd_execute(
  script,
  script_path,
  command = "bash",
  dry_run = FALSE,
  backup = TRUE,
  args = NULL,
  ...
)

cmd_run_r(
  expr,
  quoted = FALSE,
  verbose = TRUE,
  dry_run = FALSE,
  log_file = tempfile(),
  script_path = tempfile(),
  ...
)

Arguments

script: the shell script
script_path: path to run the script
command: which command to invoke; default is 'bash'
dry_run: whether to run in dry-run mode; under such mode, the shell command will not execute. This is useful for debugging scripts; default is false
backup: whether to back up the script file immediately; default is true
args: further arguments in the shell command, especially the 'FreeSurfer' reconstruction command
...: passed to system2, or additional arguments
expr: expression to run as command
quoted: whether expr is quoted; default is false
verbose: whether to print out the command script; default is true under dry-run mode, and false otherwise
log_file: where should log file be stored

Value

A list of data containing the script details:

script: script details
script_path: where the script should/will be saved
dry_run: whether dry-run mode is turned on
log_file: path to the log file
execute: a function to execute the script