Tutorials

A curated list of practical tutorials for onboarding, environment setup, and workflow execution.

Getting Started

• Basic Linux Command Lines
  Essential shell commands for file navigation, process management, and scripting basics.
• Basic SSH Usages for the CCR server
  Connect securely, transfer files, and run remote jobs on CCR resources.

Environment Setup

• How to use Miniforge
  Lightweight Conda environment setup for reproducible Python workflows.
• Python + Jupyter setup
  Configure Python and Jupyter for local or server-based analysis.
• R + RStudio setup
  Install and configure R/RStudio for statistical and genomics analysis.

Cluster and Workflow Execution

• SLURM system quickstart
  Submit, monitor, and manage jobs on the CCR cluster.
• Snakemake quickstart
  Build reproducible and scalable pipelines with Snakemake.
• CWL quickstart
  Run portable workflows with the Common Workflow Language.

Suggested Learning Path

1. Basic Linux Command Lines
2. Basic SSH Usages for the CCR server
3. Miniforge setup
4. Python + Jupyter setup or R + RStudio setup
5. SLURM system quickstart
6. Snakemake or CWL quickstart