• Jelle Treep
• Lukas van de Wiel
• Dawa Ometto
• Shiva Nadi

a computer program that provides relatively broad and direct access to the system on which it runs. The term shell refers to how it is a relatively thin layer around an operating system. A shell is generally a command-line interface (CLI) program [Wikipedia]

• Type commands to do things
• has a prompt:

jelle@localhost $ 

• Run programs and scripts
• Can be interactive or non-interactive

• Vast Majority of HPC systems are:
  • Linux based
  • Operated via Shell
• Lots of flexibility
• Not so difficult to learn
• Automation
• Git

Bash is often the default shell on Linux systems.

• Powershell (windows)
• Z shell
• many others

For now: Important to know that others do exist.

Nelle Nemo, a marine biologist, has just returned from a six-month survey of the North Pacific Gyre, where she has been sampling gelatinous marine life in the Great Pacific Garbage Patch.

• 1520 samples
• relative abundance of 300 proteins
• needs to run these 1520 files through an imaginary program called goostats.sh
• goostats.sh takes 30 seconds

We will explore the ways Nelle can achieve this in a better way. More specifically, we will learn how Nelle can automate the repetitive steps, so that her computer can work while she writes her paper.

As a bonus, once she has put a processing pipeline together, she will be able to use it again whenever she collects more data.

• navigate to a file/directory
• create a file/directory
• check the length of a file
• chain commands together
• retrieve a set of files
• iterate over files
• run a shell script containing her pipeline

The contents of this workshop are for a large part based on material of the workshop ‘The Unix Shell’ developed by the Software Carpentries and published under CC BY 4.0 license.