eWorkshop: CLI for Genomics

University of the Western Cape

10 June - 15 July, 2021

13:00 - 15:00

Instructors: Ryan Daniels

Helpers: TBC

General Information

Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Online. Get directions with OpenStreetMap or Google Maps.

When: 10 June - 15 July, 2021. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email 4078535@myuwc.ac.za for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1

Before starting Pre-workshop survey
Session 1Windows & Unix - Some Differences
Introduction to the Command Line
Session 2Navigating around & Handling Files

Day 2

Session 1Redirections & Scripting
Session 2Introduction to Project Organisation

Day 3

Session 1Introduction to High Performance Computing
Session 2Using the ILIFU HPC

Day 4

Session 1SLURM job submissions
Session 2Singularity Containers

Day 5

Session 1PLINK multi-purpose tool
Session 2Some Basic QC with PLINK

Day 6

Session 1Digging deeper with Project Organisation
Session 2Quick overview of Git
ClosingPost-workshop survey


To participate in a Data Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the Data Carpentry Genomics workshops can be found at the workshop overview site