Key concepts and tools

  • git, git clone, git push, git pull
  • SSH key authentication
  • GitHub and GitHub Classroom
  • conda, conda env create -f, .condarc
  • module load miniconda, conda activate
  • 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 a GitHub SSH key so you can push code without a password, 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 (R, Jupyter, Nextflow, Python, Snakemake) and create the nextflow_latest conda environment from the provided YAML — this environment will be activated at the start of every subsequent lab.

Setup checklist

  • Familiarize yourself with SCC OnDemand and VSCode
  • Set up an SSH key and link it to GitHub
  • Edit ~/.condarc to redirect conda package storage:
envs_dirs:
    - /projectnb/bf528/students/<your_loginname>/.conda/envs
pkgs_dirs:
    - /projectnb/bf528/students/<your_loginname>/.conda/pkgs
  • Create the course Nextflow environment:
module load miniconda
conda env create -f envs/nextflow_env.yml
conda activate nextflow_latest
nextflow -h   # confirm it installed correctly
  • Accept the GitHub Classroom link, clone the repo, make a change, and push it
  • Submit your BU email and GitHub username via the course form

Resources

Updated: