Introduction to command-line computing
2017-06-17
Introduction
Purpose: Introduce participants to the unix command line to increase efficiency and reproducibility.
Background: Scientific research, and especially scientific synthesis, requires extensive computing, which typically involves creation of hudreds or thousands of data files, analytical processes, and many products such as graphs, model outputs, maps, images, and more. Managing this complexity is often really hard, and researchers can easily lose track of just what they did, when, and why. Thus, traditional approaches to managing the research process often fail the reproducibility test, as even the original investigators can’t repeat their initial process.
- From PhDComics
Thus, the command line. The command-line provides two major advantages to the researcher:
- Repeatability
- Once you do it once, you can just re-run it
- Efficiency
- What you can do to one file, you can do to millions
These advantages come at the cost of:
- A steep learning curve (with copious esoteric terminology)
Learning outcomes
- To understand the advantages of the command line over graphical interfaces
- To understand the basic philosophy of Unix
- To learn core Unix commands for navigation and file management