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Basic Unix Command Guide
This short guide introduces a few essential Unix commands to help you navigate and work in the terminal during the workshop. You do not need to memorise everything here — just refer back when needed.
pwdPrints your current working directory.
lsShows files and folders in the current directory.
Useful options:
ls -l # long format # Note l is an alias for this in the workshop
ls -lh # human-readable sizescd folder_nameMove into a folder.
cd ..Move up one level.
cd ~Go to your home directory.
mkdir new_folderCreate a new folder.
mkdir -p path/to/folderCreate nested folders if they do not exist.
cp file.txt copy.txtcp -r folder1 folder2Copy directories recursively.
mv file.txt newname.txtmv file.txt folder/rm file.txtrm -r foldercat file.txtless file.txtUse q to exit less.
grep "pattern" file.txtSearch for text in a file.
ls *.txtMatches all .txt files.
historyUse arrow keys ↑ ↓ to navigate previous commands.
- Ctrl + C → stop a running command
- Ctrl + L → clear screen
- Tab → autocomplete
man lsShows manual pages.
These external resources provide excellent beginner-friendly tutorials:
- Software Carpentry: https://swcarpentry.github.io/shell-novice/
- The Unix Shell (Software Carpentry lesson): https://swcarpentry.github.io/shell-novice/01-intro.html
- Explain Shell (interactive): https://explainshell.com/
- Linux Journey: https://linuxjourney.com/
This guide covers the basics you need for the workshop. If something behaves unexpectedly, check your current directory with pwd and list files with ls.
- Workshop Wiki Home
- Basic Unix Command Guide
- Transcript assembly commands
- Mikado commands
- Annotation liftover commands
- Augustus
- Tiberius commands
- Helixer commands
- GALBA commands
- BRAKER3 commands
- Minos commands
- EVidenceModeler (EVM) commands
- Annotation Web Apollo Browser
- Workshop data locations
- Software tools used
- Guacamole tips
- Troubleshooting