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Monday Overview: Good-Practices in Research Coding

Goal:
Learn how to use the command line, log into the Alma HPC cluster, and set up a sensible, reproducible project folder for your research.

What We Cover

  • How to open and use the command line (Windows, Mac, Linux)
  • Basic navigation and file/folder creation: ls, cd, pwd, mkdir, touch
  • Editing files with nano and viewing them with cat
  • Logging into the Alma HPC cluster using SSH
  • Understanding login nodes vs compute nodes on Alma
  • Running interactive jobs with srun
  • Creating a simple, organized project folder for your research
  • Opening and using VSCode for coding and project management

Key Takeaways

  • The command line is a powerful tool for navigating, creating, and managing files and folders.
  • Use .gitignore to keep sensitive or unnecessary files out of version control.
  • Organize your project folders for clarity and reproducibility.
  • Use VSCode’s built-in terminal and editor to streamline your workflow.
  • Practice makes perfect—try these commands on your own!

Videos of session

Session Cheat Sheet: Monday

Basic Command Line

# Where am I?
pwd

# List files and folders
ls

# Make a new folder for practice
mkdir test_folder

# Go into it
cd test_folder

# Make a file
touch example.txt

# See the file
ls

Editing and Viewing Files

nano example.txt
# (Type your text, then Ctrl+O to save, Ctrl+X to exit)

cat example.txt

More Advanced Command Line

# See hidden files
ls -la

# Make several folders at once
mkdir -p data/{raw,processed}

# Remove a file
rm example.txt

# Go up a folder
cd ..

Logging into Alma

ssh <username>@alma.icr.ac.uk

Compute Nodes

srun --pty -t 12:00:00 --cpus-per-task 1 --mem-per-cpu 4021 --partition interactive bash
squeue -u $USER

Project Folder and VSCode

cd ..
rm -rf test_folder
mkdir biomarkers_project
cd biomarkers_project
code .

Making a Sensible Project Structure

mkdir -p data/{raw,processed} src docs results notebooks environment

Adding and Running a Script

touch process_data.sh
chmod +x process_data.sh
./process_data.sh

Homework

  • Practice basic command line commands
  • Try logging into Alma if you have access
  • Create and organize a simple project folder, and open it in VSCode

Reflection

  • What did you find easy or challenging about using the command line?
  • Were you able to log into Alma? If not, what issues did you encounter?
  • How does organizing your project folder help your research?