Intro to Makefiles - sandbox.bio

Intro to Makefiles<br>Step 1 / 25

by Stephen Bush<br>July 2026<br>In this tutorial, we’ll cover the basics of using a Makefile. If you’re familiar with<br>Snakemake, then you’re already familiar with the basic concept of a make file. Although make predates Snakemake by nearly 40 years, the basic premise is the same: Define a<br>recipe under a target, and execute the recipe by calling the target from the command<br>line.<br>Originally, make was developed to streamline the compilation of C code (don’t worry,<br>we’re not going to force you into C), and many newer tools aim to provide the same<br>functionality in a newer package. However, make remains a simple, stable staple across<br>many software projects.

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Introduction An Intro to Makefiles<br>Structure of a Rule<br>Silence is Golden<br>Rules are made to be broken<br>Fake it 'til you make it<br>Bravely default<br>Story time<br>Inclusion is not an option<br>Me first<br>Less is more?<br>Explicitly forbidden<br>A list apart<br>Change is the only constant<br>Finally! File targets.<br>Aside: Make Version and Unused Variables<br>DIY functions<br>Almost there<br>Stay on target<br>You're all clear, kid<br>One in a million<br>The end<br>The end<br>Mad Lib!<br>Exercises<br>Gzip text files<br>Ungzip text files<br>Convert and index SAM files