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Four ways to run code in a Box, from the one that needs no code of your own to the one you drive entirely from your backend. They stack, so most setups use more than one. For anything heavy or slow, do not script it at all: bake it into a template Box so it is already installed when the Box starts.

Repository setup scripts

Attached to a repository in Dashboard > Environment. Runs once when the Box starts, inside that repository’s folder, with your environment’s variables and secret files already in place.
Mark it blocking when the Box is not usable until it finishes. A blocking script delays the Box reaching ready; a non-blocking one runs alongside everything else.

Pre-commit hooks

Also per repository, run before each commit made in that repository. Mark a hook blocking to fail the commit when the hook fails.

Talking back to the Box

Setup scripts and hooks can both steer the agent running in the Box: That turns a failing hook into an instruction rather than a dead end:

Per-Box setup file

When the work differs from Box to Box, pass a local script at create time. Up to 64KB, UTF-8.
It runs in the background once the Box is ready and never delays ready. Watch it with box info:

Driving setup from your code

Configure secrets in the environment first, then run whatever you need. The script reads normal environment variables and the secret files at their configured paths, so nothing sensitive passes through the command line.
Wait for the Box to reach ready first; earlier calls are refused with a retryable box_starting. Synchronous commands cap at 600 seconds, so anything longer should detach and be polled. See Long-Running Tasks. To pipe a script that is not on the Box yet, use SSH instead. It streams stdin, stdout and stderr, so nothing has to be copied to a temporary path first:
On Windows, run this from Node, Python, WSL, Git Bash, or cmd.exe. Native PowerShell pipelines can keep stdin open for native executables, which hangs the command.