Hands-on for 'Advanced CLI in Galaxy' tutorial
The questions this addresses are:
- How can I combine existing commands to do new things?
- How can I perform the same actions on many different files?
- How can I find files?
- How can I find things in files?
The objectives are:
- Redirect a command's output to a file.
- Process a file instead of keyboard input using redirection.
- Construct command pipelines with two or more stages.
- Explain what usually happens if a program or pipeline isn't given any input to process.
- Explain Unix's 'small pieces, loosely joined' philosophy.
- Write a loop that applies one or more commands separately to each file in a set of files.
- Trace the values taken on by a loop variable during execution of the loop.
- Explain the difference between a variable's name and its value.
- Explain why spaces and some punctuation characters shouldn't be used in file names.
- Demonstrate how to see what commands have recently been executed.
- Re-run recently executed commands without retyping them.
grep to select lines from text files that match simple patterns.
find to find files and directories whose names match simple patterns.
- Use the output of one command as the command-line argument(s) to another command.
- Explain what is meant by 'text' and 'binary' files, and why many common tools don't handle the latter well.
Licence: Creative Commons Attribution 4.0 International
Keywords: data-science, bash, jupyter-notebook
Target audience: Students
Resource type: hands-on tutorial
Contributors: Avans Hogeschool, Bazante Sanders, Erasmus+ Programme, Helena Rasche, The Carpentries
Scientific topics: Software engineering