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Introduction to the linux command line

Disclaimer: Everything that is being shown and discussed during the workshop is generic and not subject-specific. Please bear with me if the examples that I choose tend to be about sequence data processing.


The workshop will consist of 2 sessions: The first session will cover the basics and end with a set of exercises for the participants to solve until session 2. There is the option to work together on these exercises in break-out rooms. Session 2 will start with sharing the solutions to the exercises from session 1. Therefore, it is stronly recommended to not attend session 1 and 2 on the same day. To accommodate all participant's availability, each session will be offered twice.

Morning (9-12) Afternoon (13-16)
Mon, 28.02.2022 session 1 break-out
Tue, 01.03.2022 session 1 session 2 (+break-out)
Thu, 03.03.2022 session 2


Session 1:

  • Finding a suitable terminal to work on
  • User environment: default shell, bash (.bashrc), environment variables ($PATH)
  • Basic linux commands: cd (file paths), pwd, man, ls (file permissions), echo (variables), cp, mv, mkdir, rm, ssh, scp, htop, du, df, time, less, cut, paste, sort, uniq, diff, cat, hexdump, wc, tr, dos2unix, touch, grep, awk, sed (regular expressions), vi, xargs, basename, ln, wget, md5sum, gzip, bzip2, tar, zless, zcat, zgrep, screen, etc.
  • Standard input (stdin), standard output (stdout), standard error (stderr), redirection, pipes
  • Autocomplete, copy/paste and recall previous commands
  • Keyboard shortcuts
  • Remote server connection
  • Monitor resource usage

Session 2:

  • Open questions session 1 and exercises
  • Loops for sequential processing (for and while loops)
  • if/else statements
  • Writing an executable bash script
  • Software installation, conda, modules
  • Q&A
  • Resumable sessions
  • SSH keys
  • If there is time: parallelization, workflow managers (snakemake), resource managers (slurm) – demo only

Course material: