Biocomputing Fall 2018, Rowan University

Introduction to UNIX



Slides can be found here

Directory

  • A folder on your computer which contains files. UNIX filesystems are organized as hierarchical directories.
  • Forward slashes divide levels in the nested hierarchy of directories, e.g. /top_level_directory/second_level_directory
  • The directory at the top of this hierarchy is called the root directory and is denoted simply as /.

Path

  • The address to a directory or file on your computer. There are, generally, two types of paths:
    • Absolute/full path represents the path of a given directory/file beginning at the root directory.
    • Relative path represents the path of a given directory/file relative to the working/current directory.
  • For example, say you have a file “my_favorite_file.txt” located in the directory /Users/myname/Desktop/my_directory.
    • The full path to this file is /Users/myname/Desktop/my_directory/my_favorite_file.txt.
    • The relative path to this file depends on where you are on the computer.
    • If you are calling this file from Desktop, the relative path would be my_directory/my_favorite_file.txt
    • If you are in /Users/myname/, the relative path becomes Desktop/my_directory/my_favorite_file.txt.

Remember - Whenever you call the full path, you can reach the file from anywhere on your computer. Relative paths will change based on your current location.

Roaming around

Command Translation Examples
cd change directory cd /absolute/path/of/the/directory/
Go to the home directory by typing simply cd or cd ~
Go up (back) a directory by typing cd ..
pwd print working directory pwd
mkdir make directory mkdir newDirectory creates newDirectory in your current directory
Make a directory one level up with mkdir ../newDirectory
cp copy cp file.txt newfile.txt (and file.txt will still exist!)
mv move mv file.txt newfile.txt (but file.txt will no longer exist!)
rm remove rm file.txt removes file.txt
rm -r directoryname/ removes the directory and all files within
ls list ls *.txt lists all .txt files in current directory
ls -a lists all files including hidden ones in the current directory
ls -l lists all files in current directory including file sizes and timestamps
ls -lh does the same but changes file size format to be human-readable
ls ../ lists files in the directory above the current one
history history see command history, and even call an earlier command with an exclamation mark and the line number (i.e !773 to reissue command #773).
echo echo print words
man manual man ls opens the manual for command ls (use q to escape page)
cat concatenate cat seqs.fasta prints the contents of seqs.fasta to the screen (ie stdout). Other options are less and more (because “less is more”, I’m sorry to say)
head head head seqs.fasta prints the first 10 lines of the file
head -n 3 seqs.fasta prints first 3 lines
tail tail tail seqs.fasta prints the last 10 lines of the file
tail -n 3 seqs.fasta prints last 3 lines
wc word count wc filename.txt shows the number of new lines, number of words, and number of characters
wc -l filename.txt shows only the number of new lines
wc -c filename.txt shows only the number of characters
grep global regular expression parser grep "a" filename.txt Search for particular strings or regular expressions in a file, in this case, search for lines with the letter “a” in the file “filename.txt”.
grep -c "a" filename.txt will COUNT the number of lines with “a” in the file
grep -v "a" filename.txt will find lines in the file WITHOUT “a”



Shortcut Use
Ctrl + C kills current process
Ctrl + L
(or clear)		 clears screen
Ctrl + A Go to the beginning of the line
Ctrl + E Go to the end of the line
Ctrl + U Clears the line before the cursor position
Ctrl + K Clear the line after the cursor
* wildcard character
tab completes word
Up Arrow call last command
. current directory
.. one level up
~ home
> redirects stdout to a file, overwriting file if it already exists
>> redirects stdout to a file, appending to the end of file if it already exists
| redirects stdout to become stdin for next command