SARS-Arena

SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development

Installation

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

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

docker pull kavrakilab/hla-arena:sars-arena

Clone this repo and run the following command in the terminal¹:

On Linux or Mac: ./start_SARS-Arena.sh

On Windows: ./start_SARS-Arena.ps1 (using PowerShell ²)

This should generate a URL with the following format:

http://127.0.0.1:8888/?token=<token_value>

Copy and paste this URL into a browser, and open the 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.

Check out the DOCUMENTATION, also provided alongside the Jupyter notebooks, for additional information on the workflows and available functions.

Enjoy SARS-Arena!

If you experience issues starting the container in the step 3 with the start script you can run the raw commands directly docker run --rm -v $(pwd):/data -p 8888:8888 --entrypoint="" kavrakilab/hla-arena:sars-arena jupyter notebook --port=8888 --no-browser --ip=0.0.0.0 --allow-root (for Linux/MacOS) or docker run --rm -v ${pwd}:/data -p 8888:8888 --entrypoint="" kavrakilab/hla-arena:sars-arena jupyter notebook --port=8888 --no-browser --ip=0.0.0.0 --allow-root(for Windows). ↩
In PowerShell, make sure you have permissions to execute the script, if you get an error_ *** cannot be loaded because the execution of scripts is disabled on this system. _follow these tips to enable running scripts. ↩