Installation¶
Welcome to the Dashing Turtle installation guide! This document will walk you through setting up and running the Dashing Turtle application, whether you’re using Windows, macOS, or Linux.
Step 1: Install ViennaRNA for putative structures¶
DashingTurtle uses the predicted reactivities as constraints in ViennaRNA to calculate putative structures.
ViennaRNA can be downloaded and installed by following the instructions: https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/install.html
Step 2: Install Docker (for the database)¶
Dashing Turtle uses a Dockerized database to store your data. You’ll need Docker installed to run it.
macOS
Download and install Docker Desktop: https://www.docker.com/products/docker-desktop
After installation, launch Docker Desktop and ensure it’s running.
Linux
Install Docker Engine following the instructions for your distribution: https://docs.docker.com/engine/install/
Step 3: Set Up the Python Environment¶
You’ll now configure the local Python environment for running the app.
1. Create a virtual environment
python3.11 -m venv myvenv
2. Activate the environment
macOS / Linux
source venv/bin/activate
3. Upgrade pip
pip install --upgrade pip
4. Install Dashing Turtle from PyPI
pip install DashingTurtle
Step 5: Run the Application¶
✔ This command will start the database in the background. ✔ Your data will persist across sessions.
dt-db up
You can now launch the application in either GUI or CLI mode:
Graphical User Interface (GUI)
dt-gui
Command-Line Interface (CLI)
dt-cli
Choose the mode that best suits your workflow.
Database Management¶
The database runs in Docker and automatically preserves your data.
To stop the database:
dt-db down
To start it again:
dt-db up
Data Output¶
All output files (landscape data, figures, etc.) are saved to:
~/DTLandscape_Output
Sample Data¶
Sample datasets are available here:
Help and Support¶
Use the –help option with CLI commands to see available options and usage:
dt-cli --help
You’re all set to begin using Dashing Turtle — happy exploring! 🚀