Trained scVI model for integrated datasets: Packer2019, Taylor 2020 (CeNGEN) and Ben-David 2021

Trained scVI model for integrated datasets: Packer2019, Taylor 2020 (CeNGEN) and Ben-David 2021

###### Simple deploy on Linux ######
## Clone the git repo on the AWS instance
git clone https://github.com/WormBase/scdefg.git
cd scdefg

## download trained model and unzip in folder
wget -q -O tmp.zip https://github.com/WormBase/scdefg/releases/download/packer2019taylor2020bendavid2021/packer2019taylor2020bendavid2021.zip && unzip tmp.zip && rm tmp.zip


## Create a Python venv in the repo main folder
python3 -m venv venv

## Activate the venv
source venv/bin/activate

## Install Python requirements
pip3 install -r requirements.txt


## launch the app and stratify the selection menu with 3 columns: `study`, `sample_description`, `cell_subtype`
python3 scdefg/app.py ./packer2019taylor2020bendavid2021 --host 0.0.0.0 --port 1337 -s study -s sample_description -s cell_subtype