🌟 Dashing Turtle Setup & Usage Guide
Welcome! This guide will help you install and run the Dashing Turtle application, even if you have little technical background. Just follow each step carefully!
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 needs a database to store your data. We use Docker to make this easy and automatic. ✅ macOS
Download and install Docker Desktop: https://www.docker.com/products/docker-desktop/
After installing, open Docker Desktop and make sure it’s running.
✅ Linux
Install Docker Engine: Docker Engine Linux install guide
✔ This will download and start the database in the background. ✔ It will keep your data even after shutting down.
🐍 Step 4: Set up Python environment (local app) ✅ Create a virtual environment
python3.11 -m venv venv
✅ Activate it
macOS / Linux:
source venv/bin/activate
✅ Upgrade pip
pip install --upgrade pip
✅ Install Dashing Turtle from PyPI
Dashing Turtle is also distributed via PyPI as DashingTurtle. Install it:
pip install DashingTurtle
💻 Step 5: Run the application
✅ Start the Database
dt-db up
✅ Graphical User Interface (GUI)
dt-gui
✅ Command-Line Interface (CLI)
dt-cli
✅ You can choose whichever mode you prefer!
🗄️ Database notes
Your database runs inside Docker and persists data between runs automatically.
You can stop it any time using:
dt-db down
To restart:
dt-db up
💬 Help
Please refer to help in the command line interface for more explanation.
🔥 Data Output Data including landscape files and figures are output to your home directory under 'DTLandscape_Output'
🔥 Sample Data for testing is available at https://github.com/jwbear/Dashing_Turtle.git
If you run into issues or need troubleshooting advice, please check our Troubleshooting Guide on Read the Docs.
🎉 That’s it!
You’re ready to use Dashing Turtle. Enjoy exploring your data! 🚀