Drupal - How to manage user permissions?

Try this command:

drush role-add-perm 'user-role' 'permission'

You can install the Permissions API

The permissions_api module provides a method for granting and revoking permissions for a given role. This module helps with the issue of staging a Drupal site across multiple environments, from development sandbox to production environment.

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Version 6.x-2.9 adds support for Drush!