common_commands.md

Common Commands

Here are common terminal commands for your use

General Terminal Commands 💻

Command	Description	Example	Notes
pwd	print working directory returns where you are in the file system	pwd	Use this anywhere to show where you are in the file system
ls	ls lists the contents of the directory you are in. Directory is the same as folder	ls	Use ls -a to show "hidden" files and directories (those that start with a period like ".config")
cd	change directory allows you to go to a different folder. cd my_folder goes from your current folder into the subfolder called "my_folder". Just entering cd will take you back to the home directory (~)!	cd my_folder	Use cd .. to go up one directory
mv	move or rename a file.	mv old_name.png new_name.png, mv foo.txt my_folder/foo.txt	Use mv to rename a file or move it to a different directory
cp	copy a file.	cp foo.txt my_folder/foo.txt	Use cp -r to copy a directory
rm	remove a file.	rm foo.txt	Use rm -r to remove a directory
mkdir	make directory.	mkdir my_folder	Use mkdir -p to make a directory and any parent directories that don't exist
rmdir	remove directory.	rmdir my_folder	Use rmdir -p to remove a directory and any parent directories that are empty
touch	creates an empty file	touch foo.txt
cat	catenate and print files.	cat foo.txt	Use cat to print the contents of a file to the terminal

Text Editors 📝

Command	Description	Example	Notes
nano	a simple terminal text editor	nano foo.txt
vim	a more advanced terminal text editor	vim foo.txt

File Permissions 🔒

Command	Description	Example	Notes
chmod	change mode of a file or directory	chmod +x foo.txt to allow the file to be executed	Use chmod to change the permissions of a file or directory
chown	change owner of a file or directory	chown user:group foo.txt	Use chown to change the owner of a file or directory

Conda 🐍

Command	Description	Example	Notes
conda create	create a new conda environment	conda create -n my_env python=3.8
conda activate	activate a conda environment	conda activate my_env
conda deactivate	deactivate the current conda environment	conda deactivate
conda list	list all packages in the current conda environment	conda list
conda install	install a package into the current conda environment	conda install numpy -c anaconda	Specify the "channel" you use with the -c flag. Find the channel why youf search it. E.g., searching "numpy conda" will show that numpy is from the anaconda channel
conda remove	remove a package from the current conda environment	conda remove numpy
mamba install	a faster alternative to conda install	mamba install numpy	Please install mamba as one of the first things you install and then use mamba install instead of conda install

Git/GitHub

• Git cheat sheets, here, here, and here
• Git official documentation

Command	Description	Example	Notes
git clone	clone a repository into a new directory	git clone [email protected]:sasank-desaraju/med-ai-workflow.git	What you use to "get" a git repository
git status	show the working tree status	git status
git pull	fetch from and integrate with another repository or a local branch	git pull	run this whenever you start working
git add	add file contents to the index	git add foo.txt, git add -A	first step to saving your changes on GitHub, git add -A adds everything in the repo
git commit	record changes to the repository	git commit -m "Added a new feature"	second step
git push	update remote refs along with associated objects	git push	third and final step
git branch	list, create, or delete branches	git branch, git branch new_feature
git checkout	switch branches or restore working tree files	git checkout new_feature
git diff	show changes between commits, commit and working tree, etc	git diff

HiPerGator 🚀

This is a SLURM-based system, so you'll need to use SLURM commands to submit jobs. Here are some common commands:

Command	Description	Example	Notes
ssh	secure shell. Connect to a remote computer using SSH	ssh [email protected]	Use ssh to connect to HiPerGator
sbatch	submit a job to the cluster	sbatch foo.sh	Use sbatch followed by a bash script (foo.sh) to submit a job to the cluster
squeue	shows the state of the jobs in the queue	squeue	Use squeuemine to show only your jobs
scancel	cancel a job	scancel 12345	Use scancel [job_id] to cancel a job
ShowAssoc	show what HPG accounts a user has access to	ShowAssoc -u albert.gator	The username is your username to learn about yourself
ShowQos	show what resources (CPUs, GPUs) an account has	ShowQos -A my_account	The account is usually your PI's HPG username or the class you're in
srun	run a command on the cluster	srun -N 1 -t 1:00:00 echo "Hello, world!"	Use srun to run a command on the cluster
sinfo	shows the state of the nodes and partitions on the cluster	sinfo	Use sinfo -N to show the nodes and their states
salloc	allocate resources for an interactive job	salloc -N 1 -t 1:00:00	Use salloc to allocate resources for an interactive job

File Transfer 📥 📤

Command	Description	Example	Notes
sftp	secure file transfer protocol. Securely transfer files between computers using SSH	sftp user@remote_host	Use sftp to transfer files between computers
scp	secure copy. Copy files between computers using SSH	scp foo.txt user@remote_host:/remote/directory	Use scp to copy files between computers
rsync	a fast, versatile, remote (and local) file-copying tool	rsync -avz foo.txt user@remote_host:/remote/directory	Use rsync to copy files between computers or directories