book

Command Line for Biologists — LaTeX source

A Practical Guide to the Terminal, Tools, and Reproducible Workflows

Structure

book/
├── main.tex              # Entry point — defines the document & includes chapters
├── preamble.tex          # All packages, styles, custom commands
├── chapters/
│   ├── 00_foreword.tex
│   ├── 01_introduction.tex
│   └── 02_terminal.tex
└── .gitignore

Building

Run pdflatex twice (the first pass builds the table of contents, the second fills in the page numbers):

pdflatex main.tex
pdflatex main.tex

Or use latexmk which figures out how many passes are needed:

latexmk -pdf main.tex

To clean up auxiliary files:

latexmk -c        # keeps the PDF
latexmk -C        # also removes the PDF

Adding a new chapter

1. Create chapters/03_your_chapter.tex starting with \chapter{...}.
2. Add \include{chapters/03_your_chapter} to main.tex (no .tex extension).
3. Compile.

Working on just one chapter (fast iteration)

Uncomment the \includeonly{} line in main.tex and list only the chapter you want to compile. Cross-references and the TOC will still know the others exist.

Custom things this project defines

• \code{...} — inline code (just \texttt, escape $, _, #, %, &, ~, \ if needed)
• \begin{reflection} ... \end{reflection} — blue callout box for reflection prompts
• lstlisting environments are styled as bash shell sessions by default. The $ at the start of a line renders in blue to highlight prompts.