DashingTurtle 0.1.9

An applicaton for building structural landscapes of RNA sequence modifications with Nanopore data.

🌟 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. ✅ Windows / 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

🔥 Step 3: Start the database

Open your terminal or command prompt, navigate to your project folder, and run:

docker compose up -d db

✔ 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

Windows:

venv\Scripts\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 ✅ 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:

docker compose down

To restart:

docker compose up -d db

💬 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

🎉 That’s it!

You’re ready to use Dashing Turtle. Enjoy exploring your data! 🚀