Shantanu Singh shntnu

Setting up a replacement Mac with Claude Code and Nix

A replacement laptop can be set up remotely when you already have a working Mac with a Nix configuration and can connect to the new machine over SSH. In this example, Claude Code ran on the existing Mac, adapted the configuration for a loaner, built the system, and deployed it to the loaner. The owner enabled access, entered passwords, and signed in to services on the laptop.

The existing setup used nix-darwin for macOS settings, Home Manager for user packages and shell configuration, Homebrew for GUI apps, and chezmoi for additional dotfiles. It also had a deploy-rs configuration for remote deployment. The procedure below describes that setup, with placeholders and adjustments for other repositories. It assumes you have permission to administer the new machine and an existing, working configuration to adapt.

marp	true
theme	default
paginate	true

Apprentices

Shantanu Singh Sr. Group Leader, Broad Institute

	# /// script
	# requires-python = ">=3.10"
	# dependencies = ["pandas", "pyarrow", "matplotlib"]
	# ///
	"""Generate the Carpenter-Singh Lab GitHub org logo from Cell Painting data.

	This is a data-derived visual mark, not a full phenotypic-profile analysis. It
	uses one matching well/profile for the requested compound (the first row with
	that perturbation name), not an aggregate across replicate plates.

	# /// script
	# requires-python = ">=3.12"
	# dependencies = [
	# "marimo",
	# "polars",
	# "pyyaml",
	# "snakemake>=9.14.6,<10",
	# "python-dotenv",
	# "loguru",
	# "cloudpathlib[s3]",

	# /// script
	# requires-python = ">=3.10"
	# dependencies = ["marimo", "ollama"]
	# ///

	import marimo

	__generated_with = "0.20.4"
	app = marimo.App(width="medium")


	═══ TURN 1 ═══
	→ sending 2 messages to qwen2.5:7b
	[0] system 'You are an agent with a bash tool. Always use the bash tool to gather informatio'
	[1] user 'How many files are in /tmp? Run a command to find out.'
	← assistant wants to call 1 tool(s):
	• bash({'cmd': 'ls -1 /tmp \| wc -l'})
	▶ running: ls -1 /tmp \| wc -l
	◀ stdout (3 bytes):
	'60\n'

	-- CompoundValet CSV: no structural identifiers → can't join to other databases
	-- Paste into https://shell.duckdb.org/
	--
	-- The Drug Repurposing Hub is a similar drug-target database but includes
	-- InChIKey, SMILES, and PubChem CID — making it instantly joinable.
	-- CompoundValet has only drug names.

	-- Load CompoundValet
	CREATE TABLE cv AS
	SELECT * FROM read_csv_auto(

	#!/bin/bash
	#
	# Calculate checksum corresponding to the entity-tag hash (ETag) of Amazon S3 objects
	#
	# Usage: compute_etag.sh <filename> <part_size_mb>
	#
	# filename: file to process
	# part_size_mb: chunk size in MiB used for multipart uploads.
	# This is 8M by default for the AWS CLI See:
	# https://docs.aws.amazon.com/cli/latest/topic/s3-config.html#multipart_chunksize