Basic Unix/Linux/OS X commands

This document covers some very basic unix commands that will be useful working with QIIME. You can find a lot of resources both on the web and as books.

Web resources

• Linux/Unix: http://www.linuxcommand.org/learning_the_shell.php
• OS X: http://acad.coloradocollege.edu/dept/pc/SciCompLab/UnixTutorial/

Books

• Unix Power Tools

cd : change directory

Change to data:

cd data

Change to your home directory:

cd

Change to one directory higher (e.g. if you’re in /home/greg/data/ change to /home/greg/):

cd ..

mv: move/rename file or directory

Rename old_filename to new_filename:

mv old_filename new_filename

wget: pull a file from a remote location

Pull the greengenes reference OTU file (4feb2011):

wget http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/Caporaso_Reference_OTUs/gg_otus_4feb2011.tgz

cp: copy a file

Copy my_file.txt to my_file.txt.backup:

cp my_file.txt my_file.txt.backup

Compress a directory to a tgz file

Compress the my_data/ directory into a single file:

tar -czf my_data.tgz my_data/

Uncompress a tgz file into the current directory

Expand the my_data.tgz file:

tar -xzf my_data.tgz

Uncompress a zip file

Uncompress the QIIME tutorial data:

unzip http://bmf.colorado.edu/QIIME/qiime_tutorial-v1.4.0.zip

Working with files

Print the first 10 lines of my_file.txt to screen:

head -n 10 my_file.txt

Print the last 10 lines of my_file.txt to screen:

tail -n 10 my_file.txt

Print all of the my_file.txt to screen:

cat my_file.txt

Open my_file.txt for editing with the pico text editor (go here for help with pico):

pico my_file.txt

View the file interactively in read-only mode. The stop viewing the file hit q:

less my_file.txt