bash_reference.qmd

---
title: Bash reference
execute: 
  enabled: false
---

## Essential commands

Knowledge of these commands is required to pass both the exercises and exam.

- `cat`: show file contents on terminal
- `cd`: change directory
  - `cd ~`: go to your home folder
  - `cd ..`: go to parent folder
- `chmod`: change permissions
- `comm`: compare two sorted files line by line
  - `comm -12`: only output lines common to both files
- `cp`: copy file/folder
- `du`: calculate file size
  - `du -h`: display file size in a human-readable format
- `echo`: display a line of text
- `grep`: find a regular expression in a text file
  - `grep -E`: use extended regular expressions
  - `grep -v`: invert sense of matching, select non-matching lines
  - `grep -o`: print only the matched part of a line
- `gunzip`: expand a file that has been compressed in GZ format; replaces the zipped file with the uncompressed file
  - `gunzip -c`: write unzipped file contents to stdout (useful for piping)
- `head`: output the first lines of a file (by default, the first 10 lines)
  - `head -5` or `head -n5`: print the first 5 lines
- `less`: display the contents of a file
- `ls`: list directory contents
  - `ls -l`: use a long listing format, i.e., one file/folder per line with additional information (permissions, owner, size, date modified)
  - `ls -a`: show all files/folders (i.e., even those starting with `.`)
- `man`: show the manual for a command
- `mkdir`: create folder
  - `mkdir -p`: when creating nested folders, also create parent folders
- `mv`: move file/folder
- `nano`: edit a text file
- `passwd`: change password
- `pwd`: output the current working directory
- `sed`: filter and transform text
  - `sed 's/foo/bar/g'`: substitute all occurrences of `foo` with `bar` ([details](bash.html#reformatting-the-ensembl-fasta-file))
- `sort`: sort lines in a text file
- `ssh user@host`: connect to a server `host` with user `user`
- `tail`: output the last lines of a file (by default, the last 10 lines)
  - `tail -5` or `tail -n5`: print the last 5 lines
- `touch`: change file timestamp; create empty file if it does not exist
- `uniq`: omit repeated lines of text
- `wc`: print newline, word, and byte counts for each file
  - `wc -l`: only print the number of lines
- `wget`: download a file


## Other commands

These commands are required for the exercises, but less important for the exam.

- `clear`: clear the terminal
- `gzip`: compress a file
- `md5sum`: calculate the MD5 checksum of a file
- `source`: run bash commands stored in a text file
- `tr`: translate or delete characters
  - `tr -d`: delete character
- `zless`: scroll through a zipped file


## Important concepts

- [permissions](bash.html#permissions)
- [pipes](bash.html#pipes)
- [file pattern matches](bash.html#file-pattern-matches)
- [regular expressions](bash.html#simple-regular-expressions)
- [while loops](bash.html#loops)