AutoGosling consists of an end-to-end pipeline that automatically interprets genomic visualization images, extracts visual encoding and view layouts, and generates Gosling (http://gosling-lang.org) visualization specifications that can be used to create similar interactive visualization for users’ own data.
This is the code repository for autogosling's webtool, consisting of the flask backend, frontend and model.
- Clone this repository
git clone https://github.com/autogosling/autogosling-tool.git
cd autogosling-tool- Go to the flask folder and download AutoGosling Yolo v7 pre-trained weights here:
cd flask
wget -O best.onnx https://drive.google.com/file/d/1x_e4V9LDgjsZhMWCnONbiQXK4Zfw6t27/view?usp=share_link- Get a GPT API key here
After getting the key, store in a .env file at the flask directory.
#.env
OPENAI_API_KEY=<paste your key here>- Create a conda environment
cd ..
conda create --name autogosling --file requirements.txt
conda activate autogosling- Start the app with script at project root
chmod 777 autogosling.sh
./autogosling.shThe front end of the app automatically runs on port 3000 with the backend on port 7777.
- Download the AutoGosling Python web-app here.
wget -O autogosling.tar.gz https://drive.google.com/file/d/1mAjrZMpZe2nAPcGiRd9KpguJvzWLKvGm/view?usp=share_link
tar -xvf autogosling.tar.gz- Go to the project directory
cd autogosling- Create a conda environment
conda create --name autogosling --file requirements.txt
conda activate autogosling- Download AutoGosling Yolo v7 pre-trained weights here:
wget -O best.onnx https://drive.google.com/file/d/1x_e4V9LDgjsZhMWCnONbiQXK4Zfw6t27/view?usp=share_link- Get a GPT API key here
After getting the key, store in a .env file at project root directory.
#.env
OPENAI_API_KEY=<paste your key here>- Run the app:
python main.pyThe app automatically runs on port 7777.