For almost all science that is currently going on today, Linux/UNIX is the operating system of choice. However, since most non-scientist type people have little or no experience with Linux, doing even the simplest things can seem daunting. Here are some basic commands and some tips to make life a little easier.

Navigation Commands

Command	Common Flags and Arguments	Example Usage	What happens
pwd	none	pwd	print working directory The directory that you are in is printed to the screen.
ls	-a -l --color Can take a path argument	ls -a -l --color	lists all the files in the current directory including "hidden" files that start with a . (-a) The files will be color coded by type (--color) and the sizes and permissions of each file will be listed (-l).
		ls *	Lists all files in the current directory as well as any files in any subdirectories
mkdir	Takes the name of the subdirectory to be made	mkdir puppy	A subdirectory named puppy has been created in the current directory
cd	Takes a relative or absolute path argument. If no argument is given it will take you to your home directory.	cd puppy	change directory You will taken to the subdirctory named puppy if it exists. If it does not exist you will be given the error message -bash: cd: puppy: No such file or directory
mv	-i Takes two file or directory arguments	mv -i file1.dat puppy/	move file1.dat has been moved into subdirectory puppy if file1.dat already exists in subdirectory puppy there will be a warning prompt asking if you want to overwrite the already existing file (-i)
		mv file1.dat file2.dat	This command is also the command used for renaming. file1.dat has been renamed to file2.dat
		mv puppy/ cat/	The directory puppy and all of its contents have been moved to a directory called cat.
Command	Common Flags and Arguments	Example Usage	What happens
Command	Common Flags and Arguments	Example Usage	What happens
Command	Common Flags and Arguments	Example Usage	What happens