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🧰 Application-Specific Help

🗂️ Overview

This PNR tutorial guides you through:

💻 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.

  1. Visit software.duke.edu
  2. Search for and check out NVivo (free for Duke users)
  3. The license key will be displayed after checkout
  4. 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:

  1. Create a Desktop shortcut for SAS

  2. Open the Start menu and search for SAS (for example, SAS 9.4).

  3. Right-click the SAS app and select Open file location.

  4. In the folder that opens, right-click the SAS icon and choose
    Show more options → Send to → Desktop (create shortcut).

  5. Edit the shortcut properties

  6. On your Desktop, right-click the new SAS shortcut and select Properties.

  7. In the Shortcut tab, locate the Target field. It will look similar to: 
    "C:\Program Files\SASHome\SASFoundation\9.4\sas.exe"
  8. At the end of that line, add a space followed by: 
    -work "P:\read_write\temp"

  9. The full Target field should now read: 

    "C:\Program Files\SASHome\SASFoundation\9.4\sas.exe" -work "P:\read_write\temp"

  10. Apply and test

  11. Click Apply, then OK.

  12. Double-click the SAS shortcut to launch SAS.
  13. In the SAS editor, enter the following command and run it: 
    %put %sysfunc(pathname(work));
  14. Confirm the log output begins with: 
    P:\read_write\temp\

📈 Stata

Stata can be installed on PNR 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.

🛠️ 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
  • 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

  1. In your PNR Windows VM, click the ✏️ pencil icon to install:
  2. Conda

  3. Visual Studio Code (VSCode)

  4. Once installed, open VSCode

  5. Use the menu to open a new CMD prompt terminal (not PowerShell or Bash).
  6. Run the following command to activate conda (base): C:\ProgramData\miniconda3\Scripts\activate.bat
  7. Now in the same CMD prompt terminal run: conda init cmd.exe (disregard message 'Operation Failed' this is expected, continue to the next step)
  8. Close the CMD prompt terminal. Now when you launch a CMD prompt terminal you will be able to activate conda: conda activate

🖥 Set Command Prompt as the default terminal in VSCode

  1. In VSCode press Ctrl + Shift + P.
  2. Type Terminal: Select Default Profile and press Enter.
  3. Select Command Prompt or Command Prompt (Conda) from the list.
  4. Now when you press Ctrl + ` (control and the backtick key) to open a new terminal and it defaults to Command Prompt.

🔧 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>

🧪 Create Conda Environment (example)

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

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

Python/Jupyterlab Extensions

To get Python or JupyterLab .vsix extension files for install in VSCode please request via ticket after choosing PNR Project Software Request: Request Help

Once your ticket is complete 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-<version>.vsix)

Or via terminal:

From the folder where you placed the .vsix files, run in a terminal:

code --install-extension ms-python.python-<version>.vsix
code --install-extension ms-toolsai.jupyter-2024.10.2024100401-win32-x64.vsix
Replace <version> with the filename in your folder. Note: For compatibility with VSCode version, you must use JupyterLab extension version: 

ms-toolsai.jupyter-2024.10.2024100401-win32-x64.vsix

Setting up JupyterLab in VSCode (after installing the JupyterLab extension (see above))

  1. Create a new conda environment 
    conda create -n jupyter_test python=3.11 -y
conda activate jupyter_test
  2. Install Jupyter kernel support (conda-only) 
    conda install ipykernel jupyter_core jupyter_client -y
  3. Register the environment as a kernel 
    python -m ipykernel install --user --name jupyter_test --display-name "Python (jupyter_test)"
  4. Verify the kernel is registered 
    jupyter kernelspec list
    You should see something like: 
    Available kernels:
  python3       C:\Users\<netid>\.conda\envs\jupyter_test\share\jupyter\kernels\python3
  jupyter_test  C:\Users\<netid>\AppData\Roaming\jupyter\kernels\jupyter_test
  5. Create a new file: test.ipynb.
  6. In the top right, click Select Kernel → choose Python (jupyter_test).
  7. Run a cell like: 
    print("Hello, world!")
  8. Check for output below the cell, if you see Hello, world! the setup is done.

📊 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.