kavrakilab/hla-arena

By kavrakilab

Updated almost 3 years ago

A customizable environment for the structural modeling and analysis of peptide-HLA complexes

Image

591

HLA-Arena installation

  1. If you don’t already have it, install Docker.

    Docker for Mac or Windows: https://www.docker.com/products/docker-desktop

    Docker for Linux: https://docs.docker.com/install

  2. In a command prompt, pull the HLA-Arena image from Docker Hub by typing:

     docker pull kavrakilab/hla-arena
    
  3. Create a folder in which you want to run the workflows (optional).

     mkdir workflows; cd workflows
    
  4. Copy HLA-Arena notebooks and associated data to your local machine by typing:

     docker run --rm -v $(pwd):/temp --entrypoint cp kavrakilab/hla-arena /hla_arena_data/data.tar.gz \
     /temp/; tar -xzvf data.tar.gz
    
  5. Run HLA-Arena in this folder by typing:

     docker run --rm -v $(pwd):/data -p 8888:8888 --entrypoint="" kavrakilab/hla-arena jupyter \
     notebook --port=8888 --no-browser --ip=0.0.0.0 --allow-root
    
  6. This should generate a URL with the following format:

     http://127.0.0.1:8888/?token=<token_value>
    
  7. Copy and paste this URL into a browser, and open any available Jupyter notebook (i.e., one of the files with extension .ipynb). Note that all the data created in the container will be saved inside sub-directories of the current folder.

  8. Check out the DOCUMENTATION, also provided alongside the Jupyter notebooks, for additional information on the workflows and available functions. And check our github repository for tutorials and updates.

    Enjoy HLA-Arena!

Docker Pull Command

docker pull kavrakilab/hla-arena