Linux Intro and Command-Line Basics

Intro

The Linux command line uses a variety of flavors of 'Unix', an operating system first developed in the 1960s. In general, the unix command format is as follows:

command argument1 argument2 --option1name option1value ...

E.g, you can use the --help option, which nearly every command has, to query the usage for the copy command, cp, with:

cp --help

You can think of every command like a shortcut - the actual functionality of the command is located in code elsewhere from your 'current location' on DynoSparky - but by evoking its name you request that code to be executed. If you are entirely new to Unix, you may find Andrew Jahn's Unix for Neuroimagers to be an extremely comprehensive resource. "This will be a new language to you, and as with any language, the beginning can be disorienting and overwhelming at times; however, stick with it, and I promise that the fog will begin to clear eventually, and you will discern what exactly it is you need to know when searching the help manuals, and what it is that you can disregard."

Cheat Sheet

Command	Description
ls	Lists all files and directories in the present working directory
ls -a	Lists hidden files as well
ls -l	Lists vertically with detailed information
ls -la	You can combine flags like so!
ls -l *	List each subfolder in a directory
ls -d /path/to/files/sub-*/ses-*/func	List the relative paths of all of the matching folders
cd ~	Navigate to $HOME directory
cd ..	Navigate one level up
cd <path>	Navigate to
pwd	Prints the full path of the current directory
cat <file>	Prints the contents of a file
mv <source> <destination>	Move a source file or rename to destination
cp <source> <destination>	Copy a source file to destination
cp -r <source> <destination>	Copy a source folder to a destination
rm <file>	Permanently delete a file
rm -r <folder>	Permanently delete a folder
sudo	Placing 'sudo' in front of a command is like running as administrator
clear	Clears the terminal window
echo $VARIABLE	Displays value of variable
ssh -Y user@remoteaddress	Connect remotely to a server via secure shell
ssh -X -Y user@remoteaddress	Start SSH connection with X11 forwarding (graphical applications run locally)
touch <filename>	Create an empty file, at
echo "sometext"	Print "sometext" to standard output
echo "sometext" >> <filename>	Append "sometext" to file
echo "sometext" > <filename>	Write "sometext" from scratch to file
nano <filename>	Edit a file in the nano text editor
vim <filename>	Edit a file in the vim text editor
grep "filterkey"	Filters a standard output for lines containing "filterkey"
CTRL-c	Stop current command

These are just a few and some of the most powerful / common of many built-in commands.

Software Environment

C Shell Configuration File

.cshrc is a file that is executed each time you execute a new shell (i.e., each time you log in, open a new Remote Desktop session or Xterm window). .cshrc Docs

You can take advantage of .cshrc to built yourself shortcuts, aliases, and set up user configurations.

E.g., if you're constantly using the command ls -l instead of regular ls, and it's becoming tedious to type in, you can add a line in your .cshrc which builds an alias for you:

alias l 'ls -l'

Then after either relaunching a session, or running source ~/.cshrc to load the file, you can use l in lieu of ls -l.

Virtual Environments

venv

One important environment we make use of in the LCBD is venv. Like other systems, such as anaconda, a virtual env

anaconda

Docker

Docker is a software we have access to on DynoSparky, which allows us to build, run, and store "containers". Many software for data analysis are offered via Docker containers, which are packaged applications that make the execution of the software much more straightforward and consistent.

For example, when the latest releases of MRIQC, FMRIPREP, and LCBD scripts all rely on different versions of the PyDicom package, a Docker container works as a solution. In the figure below, Docker containers are represented on the left, and virutal machines on the right.