MHCnuggets batch container

The MHCnuggets batch container allows the a docker container to spin up, run the predict module, provide the output, and then the container shuts down when completed. You can use either the docker-compose approach, or the docker run approach.

1. Create a new and empty directory on your workstation, and change into that directory. From inside of the empty directory clone the repository to your workstation (currently it's a specific git branch):

git clone https://github.com/KarchinLab/mhcnuggets

2. Change directories to the mhcnuggets directory that was just cloned:

cd mhcnuggets/

3. Run the following command from within the same directory as the Dockerfile to build the docker image:

sudo docker build -t mhcnuggets_batch .

Method 1 - Docker Compose

1. While still in the same directory that docker-compose.yml resides in, run the following command to start the docker container, and you should see the output in your console:

sudo docker-compose up

2. Modify the environment variables in the docker-compose.yml file as required, and re-run the command. The sample docker-compose.yml file has the available environment variables present and commented out.

Method 2 - Docker Run

1. While still in the same directory that you can see the mount directory in, run the following command, and you should see the output in your console:

sudo docker run -v `pwd`/mount:/mhcnuggets/mount mhcnuggets_batch -c I -p /mhcnuggets/mount/test_peptides.peps -a 'HLA-A02:60'

2. Modify the command line arguments as required.

3. For help on the available command line arguments, run this command:

sudo docker run -v `pwd`/mount:/mhcnuggets/mount mhcnuggets_batch -h