Computing Environments: Linux, Bash, Docker, and Tooling

Effective data science in R often relies on Unix/Linux command-line environments, shell scripting (bash), text editors (vi, emacs), and containerized runtime environments (Docker, Guix).

---

1. Linux Operating System & bash Shell

Linux is the underlying operating system organizing compute clusters, servers, and cloud instances. Commands in Linux are executed via a “shell” language. The primary shell for Linux is the Bourne Again Shell (bash):

• Shell Manuals & History:
  • Bourne Again Shell (bash) Wikipedia
  • GNU bash Manual
  • Chet Ramey: Usenix Article on bash
• Tutorials & Reference Guides:
  • Linux.org Beginner Tutorials ⚠️
  • Wikipedia History of Linux
  • The Linux Documentation Project (TLDP) ⚠️
  • University of Surrey Unix/Linux Tutorial for Beginners
• Video Overviews:
  • The Origins of Linux (Linus Torvalds)
  • Basic Linux Tasks

---

2. Containerized Environments: Docker & GNU Guix

Docker and GNU Guix ⚠️ provide mechanisms for building, running, and sharing isolated software “containers”. They eliminate “works on my machine” discrepancies and enable reproducible compute pipelines.

Docker

• Multiplatform containerization engine.
• A Hands-On Introduction to Docker
• AntiSMASH Biological Container

GNU Guix ⚠️

• Purely functional package manager and system distribution that does not require root permissions for user installs.
• Offers transactional upgrades, roll-backs, and per-user profiles.
• Guix Notes (Pjotr Prins)
• Reproducible Software Environments in HPC with Guix (Courtès & Wurmus)
• GNU Guix in an HPC Environment (Ricardo Wurmus)

---

3. Editors & Historical Statistical Software Tools

• Command-Line Editors:
  • GNU Emacs ⚠️
  • Vim / vi Visual Editor ⚠️
• Document Rendering & Typesetting:
  • LaTeX Document Preparation
  • Utilities for DVI and PostScript viewing: xdvi, dvips, ghostview.
• Statistical Software Directories:
  • ASA Statistical Software Guide ⚠️
  • Statistical Reporting with S/R (Frank Harrell) ⚠️