Skip to main content

Tufts HPC Quick Start Guide

Welcome to the Tufts-specific documentation for the tucca-rna-seq workflow! These guides provide essential information for using the workflow on the Tufts High-Performance Computing (HPC) cluster.

Start Here

This guide provides Tufts-specific quick start information. For complete installation and setup instructions, see the main Installation Guide first.

This guide covers the essential Tufts-specific steps to get you running the tucca-rna-seq workflow on the Tufts HPC cluster quickly.

Prerequisites​

1. Tufts HPC Account​

You need a Tufts Cluster Account to access the HPC cluster:

Requirements:

  • Valid Tufts Username and Password
  • Faculty or researcher sponsorship (for guest/student accounts)
  • Approval process takes multiple business days

Quick Setup Steps​

1. Connect to Tufts HPC​

SSH Access (Recommended):

ssh your_utln@login.tufts.edu

VSCode Remote Development (Highly Recommended):

2. Get Off Login Node​

# Request interactive compute node
srun -p interactive --pty bash

3. Load Required Modules​

# Purge all currently loaded modules
module purge

# Load required modules for tucca-rna-seq
module load snakemake/8.27.1
module load singularity/3.8.4
module load miniforge/24.11.2-py312

4. Navigate to Lab Workspace​

# For Kaplan Lab users
cd /cluster/tufts/kaplanlab/your_utln

# For other labs
cd /cluster/tufts/your_lab/your_utln

# Create project directory
mkdir my_rnaseq_project
cd my_rnaseq_project
Set Up a Shared Software Cache!

Your home directory on the cluster has a strict storage quota. To avoid errors and speed up future analyses, we strongly recommend setting up a permanent, shared cache for software environments in your lab's shared workspace before you run the workflow for the first time.

See the HPC Best Practices Guide for detailed instructions.

5. Clone and Setup Workflow​

For detailed instructions on cloning the repository and setting up the workflow's dependencies, please follow the main Installation Guide.

After cloning, you will need to configure the workflow for your specific analysis. This includes editing the main config.yaml file and associated sample sheets, as well as customizing the slurm execution profile to add your email for job notifications.

For detailed instructions, please refer to the main Configuration Guide.

Tufts-Specific Resources​

Documentation​

Support​

Next Steps​

After completing this quick setup:

  1. Follow the main Installation Guide for complete workflow setup
  2. Configure your analysis using the Configuration Guide
  3. Run your workflow following the Running Guide

For complete documentation, always refer to the main guides first, then use this quick start for Tufts-specific details.

Last updated on by benjibromberg