🧰 Application-Specific Help

🗂️ Overview

This PNR tutorial guides you through:

Installing Applications on a Windows VM
Installing Applications on a Linux VM

💻 Working with Your VM in a PNR Project

All Members in a PNR project can build a personal Windows or Linux VM. These VMs can be easily deleted and recreated, allowing you to use the right tools at each phase of your project.

🪟 Part 1: Installing Applications on Your Windows VM

Researchers can install software via self-service by clicking the ✏️ pencil icon next to the Launch Desktop button:

Software Install

For best performance, only install the software you need for the current phase of your project. You can delete and recreate your VM later to install other tools.

After checking the boxes for desired software, click Install. You will receive an email confirmation once the installation is complete.

🧠 NVivo

NVivo is available in the PNR but requires a license key upon first use and annual renewal.

Visit software.duke.edu
Search for and check out NVivo (free for Duke users)
The license key will be displayed after checkout
Launch NVivo → Enter the license key when prompted

📊 SAS

Setting the Work Library Path

To avoid "insufficient resources" errors caused by temporary files filling your C: drive:

Drag SAS from your Start Menu to the Desktop

Right-click the shortcut → select Properties

In the Target field, append:
```
-work "P:\read_write\temp"
```

Temp files will now go to your P: drive:

📈 Stata

Stata/SE 18 can be installed on SAFER Windows VMs, but it requires a valid license.

🧾 Step 1: Purchase a License

To obtain a license, visit:
🔗 software.duke.edu

Search for and check out Stata/SE 18.

🛠️ Step 2: Submit a Help Ticket

Once you have your license details, please submit a Get Help ticket so an RC Admin can apply the license for you.

📩 In your ticket, include the following information:

Licensed software: Stata/SE 18
License type: (e.g., Single-user, Network, etc.)
License term: (e.g., Annual, Perpetual)
Serial number:
Code:
Authorization:

📎 Note: You must unzip any files before importing them into Stata.

🐍 Python

⚙️ Conda Setup

✅ You can use the CMD Prompt that comes with the Miniconda install.
You can find it in the Start Menu as Anaconda Prompt — this has everything configured automatically.
Alternatively, follow the manual steps below if you prefer to work inside VSCode.

🛠️ Install Conda and VSCode

In your PNR Windows VM, click the ✏️ pencil icon to install:
Conda
Visual Studio Code (VSCode)
Once installed, open VSCode
Use the menu to open a new CMD prompt terminal (not PowerShell or Bash).
Run the following command to activate conda (base): C:\ProgramData\miniconda3\Scripts\activate.bat

🧪 Create Conda Environment (example)

To avoid dependency issues, best practice is to work in a clean, isolated environment:

Open a new CMD prompt terminal in VSCode
Run the following command to activate conda (base): C:\ProgramData\miniconda3\Scripts\activate.bat
Create the environment: conda create -n torch-env python=3.10
Activate the environment: conda activate torch-env

🧠 Tip: You can list all conda environments at any time with: conda env list

🔥 e.g., Install PyTorch (CPU-Only)

conda config --add channels conda-forge
conda config --add channels pytorch
conda config --add channels nvidia
conda config --set channel_priority strict
conda install pytorch cpuonly -c pytorch

🧩 Visual Studio Code (VSCode)

Python Extension

To get the Python .vsix extension file for install in VSCode place a ticket and choose PNR Project Software Request: Request Help

To install your extension .vsix file:

Open VSCode
Press Ctrl+Shift+P
Run Extensions: Install from VSIX
Select the .vsix file (e.g., P:\transfer\to_project\ms-python.python-*.vsix)

🔧 Set Conda and Interpreter in VSCode Settings

To make Miniconda the default Python interpreter and automatically activate the base environment in every terminal:

1. Open VSCode Command Palette

Press: Ctrl + Shift + P
Then type: Preferences: Open User Settings (JSON)
Select it.

2. Copy and paste this into the `settings.json` file

{
  "python.defaultInterpreterPath": "C:\\ProgramData\\miniconda3\\python.exe",
  "terminal.integrated.profiles.windows": {
    "Command Prompt (Conda)": {
      "path": "C:\\Windows\\System32\\cmd.exe",
      "icon": "terminal-cmd",
      "args": [
        "/K",
        "C:\\ProgramData\\miniconda3\\Scripts\\activate.bat && conda activate base"
      ]
    }
  },
  "terminal.integrated.defaultProfile.windows": "Command Prompt (Conda)"
}

3. Save and Reload

Save the file: Ctrl + S
Reload VSCode: Ctrl + Shift + P → Reload Window (or close VSCode and reopen)

4. Open the Terminal

Press: Ctrl + `
You should now see the terminal open with: (base) C:\Users\yourname>

🖥 Set cmd.exe as Default in VSCode

Open VSCode
Go to Settings (Ctrl + ,)
Search for: default profile
Set Terminal › Integrated › Default Profile: Windows to: Command Prompt (Conda)

📊 R and RStudio Configuration

Even with proxy set at install, R needs internal proxy settings:

# Set CRAN repo
myrepo = getOption("repos")
myrepo["CRAN"] = "http://cran.r-project.org"
options(repos = myrepo)
rm(myrepo)

# Set Proxy
Sys.setenv("http_proxy"="http://safer-proxy.oit.duke.edu:3128")
Sys.setenv("https_proxy"="http://safer-proxy.oit.duke.edu:3128")

To debug install issues:

options(internet.info = 0)  # Turn on
options(internet.info = 2)  # Turn off

🧠 In RStudio

Run the same commands in the console.

Use install.packages("YourPackageName") to install.

🔁 These settings must be re-applied each session.

🐧 Part 2: Installing Applications on Your Linux VM

For software installation please submit a ticket: Request Help.

Approved software includes:

7Zip
Adobe Acrobat Reader
Miniconda
Git / GitLab
Matlab R2023a
Microsoft Office
R / RStudio
NVivo
SAS 9.4
StataSE (licenses required)

🔐 Set Duke Network Proxy

Open a terminal and run the following:

export https_proxy="http://safer-proxy.oit.duke.edu:3128"

export http_proxy="http://safer-proxy.oit.duke.edu:3128"

🛠️ Creating and Using a Conda Environment