I often need to run routines (that might take a long time) from the command line.  For example, a nightly import of thousands of records.  I did this all the time in Drupal 7, but initially couldn't figure out how I should set it up in Backdrop CMS.

(For those that don't know, Backdrop is a fork of Drupal 7, but currently being maintained and with new features added on.)

Here's how you need to set it up in Backdrop CMS:

First: Create a "/routines" directory, and add this .htaccess file to it (so no one can run your routine from the web):

# Turn off all options we don't need.
Options -Indexes -ExecCGI -Includes

# Set the catch-all handler to prevent scripts from being executed.
SetHandler Drupal_Security_Do_Not_Remove_See_SA_2006_006
<Files *>
  # Override the handler again if we're run later in the evaluation list.
  SetHandler Drupal_Security_Do_Not_Remove_See_SA_2013_003
</Files>

# If we know how to do it safely, disable the PHP engine entirely.
<IfModule mod_php5.c>
  php_flag engine off
</IfModule>
<IfModule mod_php7.c>
  php_flag engine off
</IfModule>
<IfModule mod_php.c>
  php_flag engine off
</IfModule>

# Deny all requests from Apache 2.4+.
<IfModule mod_authz_core.c>
  Require all denied
</IfModule>

# Deny all requests from Apache 2.0-2.2.
<IfModule !mod_authz_core.c>
  Deny from all
</IfModule>

Next, create a my_routine.php file (named whatever) in that directory which is your routine:

<?php

// Begin by defining the location of your backdrop root directory.
// Here we assume this file is located in backdropdir/routines/file.php.  If not, simply set
// this variable to exactly what the directory path is.  Ex:  /var/www/html/backdrop
define('BACKDROP_ROOT', dirname(dirname(__FILE__)));

// Change the directory to the Backdrop root.
chdir(BACKDROP_ROOT);

include_once BACKDROP_ROOT . '/core/includes/bootstrap.inc';
backdrop_bootstrap(BACKDROP_BOOTSTRAP_FULL);


// Double-check to make sure we are running this script from the command line and not the web
if (php_sapi_name() !== 'cli' && php_sapi_name() !== 'cgi-fcgi') {
  die("Sorry, this script is only meant to be run from the command line.");
}


/////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////
// At this point, you should have full access to all the backdrop functions as well as all
// module functions.  Ex: node_load(), db_query(), my_module_xyz(), etc.


$start = time();
print "\n -- Starting routine -- \n";


// TODO: DO CODE HERE.



// All done-- print how long it took us to the command line.
print "\n -- Finished routine in " . (time() - $start) . " seconds. \n\n";

From crontab or on the CLI, run your routine with:

php /path/to/backdrop/routines/my_routine.php

Easy peasy.

Hope this helps someone!