Some dependencies require that pytorch is already installed:
pip install torch
After that, you can install the prediction system and web framework:
pip install -r backend/requirements.txt
Chebifier comes with a number of mandatory configuration files. config.template.json contains a template for a Chebifier configuration. Copy the contents of this file
cp backend/config.template.json backend/config.json
and change the path for each setting according to your setup.
- ELECTRA_CHECKPOINT : Path to a chebai-electra checkpoint,
- BATCH_SIZE: Number of molecules that are passed to the model at once,
- CLASS_HEADERS: Mapping of prediction labels to ChEBI classes,
- CHEBI_JSON: Hierarchy of labels defined in
CLASS_HEADERS(this file can be generate with robot export using the options--header "ID|LABEL|SubClasses" --entity-format ID)
Change to the respective directory and build the node.js files
cd react-app
npm run build
You can now start the development server with
cd backend
flask run
The server should now run at localhost:5000