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Desktop Application

PIPA provides native desktop installers for Windows, Linux, and macOS. The desktop app wraps the web interface in a native window and automatically starts the Flask backend when launched.

Download

Download the latest installer for your platform from the GitHub Releases page.

Platform File Architecture
macOS (Apple Silicon) PIPA_x.x.x_aarch64.dmg M1, M2, M3, M4
macOS (Intel) PIPA_x.x.x_x64.dmg Intel Macs
Windows PIPA_x.x.x_x64-setup.exe or PIPA_x.x.x_x64_en-US.msi 64-bit Windows 10/11
Linux (Debian/Ubuntu) pipa_x.x.x_amd64.deb 64-bit Debian-based
Linux (Universal) pipa_x.x.x_amd64.AppImage Any 64-bit Linux

Installation

macOS

  1. Download the .dmg file for your Mac (Apple Silicon or Intel)
  2. Open the .dmg file
  3. Drag PIPA to the Applications folder
  4. On first launch, right-click the app and select Open (macOS Gatekeeper may block unsigned apps)

macOS Security

If macOS shows "PIPA can't be opened because it is from an unidentified developer", go to System Preferences > Security & Privacy > General and click Open Anyway.

Windows

  1. Download the .exe installer or .msi package
  2. Run the installer and follow the setup wizard
  3. PIPA will be available in the Start Menu

Windows Defender

Windows SmartScreen may warn about an unrecognized app. Click More info > Run anyway.

Linux

Debian/Ubuntu (.deb):

sudo dpkg -i pipa_2.0.0_amd64.deb
sudo apt-get install -f  # install any missing dependencies

Any Linux (.AppImage):

chmod +x pipa_2.0.0_amd64.AppImage
./pipa_2.0.0_amd64.AppImage

Prerequisites

The desktop app provides the graphical interface, but the bioinformatics tools must be installed separately. You have two options:

Install all tools via Conda/Mamba:

# Download the environment file from the PIPA repository
curl -O https://raw.githubusercontent.com/lcerdeira/Pipa/main/environment.yml

# Create the environment
conda env create -f environment.yml
conda activate pipa

Then launch PIPA desktop — it will detect the tools on your PATH.

Option B: Docker Backend

Run the backend with all tools in Docker, and use the desktop app as the frontend:

# Start the backend with all bioinformatics tools
docker-compose up -d

# Then open the PIPA desktop app — it connects to localhost:5000

Option C: Individual Tool Installation

Install tools manually using your system package manager:

Ubuntu/Debian: 

sudo apt-get install prokka mlst barrnap
pip install abricate

macOS (Homebrew + Bioconda): 

brew install brewsci/bio/prokka
conda install -c bioconda mlst barrnap abricate spades flye

Troubleshooting

"Flask backend failed to start"

The desktop app tries to start Flask automatically. If it fails:

  1. Make sure Python 3 is installed and on your PATH
  2. Install Flask: pip install flask flask-cors
  3. Or start Flask manually: 
    cd /path/to/Pipa/back-end
pip install -r requirements.txt
flask run --host 0.0.0.0 --port 5000
  4. Then open the PIPA desktop app

"Connection refused" or blank screen

The app connects to http://127.0.0.1:5000. Make sure:

  • Flask is running on port 5000
  • No firewall is blocking localhost connections
  • Try opening http://127.0.0.1:5000/api/jobs in your browser to verify

macOS: "App is damaged and can't be opened"

Run this in Terminal: 

xattr -cr /Applications/PIPA.app

Linux: AppImage won't start

Make sure FUSE is installed: 

sudo apt-get install fuse libfuse2

Building from Source

If you want to build the desktop app yourself:

# Prerequisites: Node.js 18+, Rust, Cargo
cd UI/DesktopPIPA

# Install dependencies
yarn install

# Build the web SPA
npx quasar build

# Build the Tauri desktop app
npx @tauri-apps/cli build

The installer will be in src-tauri/target/release/bundle/.