This lab and all labs will provided via a link in an announcement on the Blackboard page.

Key concepts and tools

  • git, git clone, git add, git commit, git push, git pull, git log
  • SSH key authentication (SCC and laptop)
  • GitHub as a shared remote — push from one machine, pull on another
  • conda, conda env create -f, .condarc
  • module load miniconda, conda activate
  • NXF_SYNTAX_PARSER=v2 — strict Nextflow syntax parser required for static typing
  • SCC OnDemand, VSCode on a compute node
  • HPC concepts: head node vs. compute node, home directory vs. project directory

This lab covers the foundational tooling used throughout the semester. You will configure your SCC account, set up GitHub SSH keys on both the SCC and your laptop, and redirect your conda package storage to /projectnb/bf528/students/<username> to avoid filling up your home directory quota. You will install the required VSCode extensions and create the nextflow_latest conda environment (Nextflow) — this environment will be activated at the start of every subsequent lab.

The git activity demonstrates the core model: GitHub is a shared remote, not a copy of your code. You push commits from one machine so another machine can pull them. You will make a change on the SCC, push it to GitHub, clone the repo on your laptop, then push a second change from the laptop and pull it back on the SCC. You will follow-up by intentionally introducing a small merge conflict and learning how to resolve it using the merge editor.

Learning Objectives

Perform a complete edit–commit–push–pull cycle and resolve a merge conflict

Purpose - Why This Matters: Every subsequent lab and project assumes you can move code between instances without losing work or overwriting changes unnecessarily

Task - What you will do: Set up an SSH key on the SCC and link it to GitHub for easy authentication. Practice editing and committing changes in a GitHub repository across multiple instances.

Criteria - How you’ll know you’re succeeding: You can explain the purpose of each of the commonly used git commands. You understand the basics of pushing, and pulling by resolving a simple merge conflict.

Set up a portable, reproducible conda environment on the SCC

Purpose - Why This Matters: While many of these steps are specific to our SCC architecture, their underlying concepts are agnostic and universally important. Understanding how to set up a basic conda environment to provide an isolated instance of a software package and all of the associated setup will be translatable to other HPC and development environments.

Task - What you will do: Direct conda to store downloaded packages and files to dedicated project disk space outside of your home directory. Create a basic conda environment containing the latest version of Nextflow for use throughout the semester.

Criteria - How you’ll know you’re succeeding: When the conda environment is activated, you can run a basic nextflow command (nextflow -h) to demonstrate its proper installation. All conda related packages are stored in a directory you create in the project disk space, not your home directory (you can manually check your ~/.condarc file).

First Lab Instructions

Since you have not setup the first lab, you will be given instructions here on how to get started. In future labs, you will simply accept the classroom link and then clone the repo and work from there.

On Blackboard, please click on the link provided that will give you access to a repository containing all of the lab01 materials, and follow the on-screen GitHub Classroom prompts to accept the assignment.

Explore the Repo in Your Browser

You have not set up an SSH key yet, so do not try to clone the repository onto the SCC just yet — it will fail. Instead, stay in your browser: open the repository GitHub Classroom just created for you and read through the lab-01 materials directly on GitHub.com.

Clone the Repo onto the SCC and Work on the Git Exercise

Once you have generated an SSH key on the SCC and added it to your GitHub account as part of the steps in the repo, start a VSCode session on the SCC and open it to your student directory: /projectnb/bf528/students/<your-username>/ (replace <your-username> with your BU login, without the @bu.edu).

Go to your repository’s page on GitHub and click the green <> Code button to copy its SSH clone URL, then run the following command to clone it into your student directory:

git clone git@github.com:.../your-repo.git      # the link will look slightly different

Complete the rest of the exercise in your cloned repository, following the instructions in its README.md.

AIAS Level Expectations (AIAS Levels 1-5)

You may use AI freely for this lab at anywhere from levels AIAS 1-5 depending on your background. The specifics of this lab are not important as every environment setup will be slightly different: the important takeaways are the high-level concepts of how these tools allow for reproducibility and portability and why we care to use them.

Additional Resources

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