PlantSingleCell

🌱 PlantSingleCell 2025 – Day 1 Session 2 Setup Guide

Welcome to Session 2 of the PlantSingleCell 2025 Workshop! This guide walks you through setting up your environment and starting your analysis using RStudio on VT ARC’s OOD platform.

---

🎯 Objective

The goal of this session is to help you set up a reproducible and high-performance computing environment for integrating single-cell plant data using R. You will learn how to:

• Access and clone the workshop repository
• Launch and configure RStudio on the Virginia Tech ARC cluster
• Set up a dedicated R environment and working directory
• Begin analysis using scripts provided in the Day1Section2-Integration folder

---

📁 Step 1: Get the Scripts

1. Create your working directory:

   mkdir -p /projects/songli_lab/PlantSingleCell2025/Day_1/ParticipantFolder/[dir_name]
   cd /projects/songli_lab/PlantSingleCell2025/Day_1/ParticipantFolder/[dir_name]
   

2. Clone the repository:

   git clone https://github.com/LiLabAtVT/PlantSingleCell.git
   

3. Navigate into the Integration directory:

   cd PlantSingleCell/Day1Section2-Integration
   

---

💻 Step 2: Launch RStudio on VT ARC

Go to 👉 https://ood.arc.vt.edu/pun/sys/dashboard and click on RStudio.

📌 RStudio Launch Settings:

• Cluster: OWL - Water-cooled AMD CPU
• Partition: normal_q
• Account: introtogds
• Run Time: 2 hours
• Version: RStudio 2024.12.0 / R 4.4.2
• Cores: 12

⚙️ Advanced Options:

• Override Memory (GB): 256
• Extra Modules:

  GSL/2.7-GCC-13.2.0
  HDF5/1.14.3-gompi-2023b
  

👉 Click Launch, and once the status changes to Running, hit “Connect to RStudio Server”.

---

🧪 Step 3: Prepare the R Environment

In the Console tab of RStudio, run the following:

1. Set your R library path:

   Sys.setenv(R_LIBS_USER="/projects/songli_lab/PlantSingleCell2025/Day_1/Session_2/env/")
   .libPaths(Sys.getenv("R_LIBS_USER"))
   .libPaths()  # Confirm the change
   

2. Set the working directory:

   setwd("/projects/songli_lab/PlantSingleCell2025/Day_1/ParticipantFolder/[dir_name]/PlantSingleCell/Day1Section2-Integration")
   

---

🚀 Step 4: Start Your Analysis

You’re all set! 🎉 Start running the commands provided in the scripts and begin exploring your data.

Happy analyzing! 🍀