Setup

MntJULiP doesn't necessarily need a Dockerfile, since it is a python package and you could use virtualenv, however, there might be issues with the cmake version on the clusters so it's better to use Docker anyways.

Here's the Dockerfile that should be saved and run in the MntJULiP source folder:

FROM python:3.7

WORKDIR /home

RUN apt-get update -qq && apt install -y cmake

COPY . .

RUN python setup.py install

Running

Start by following the instructions here: https://github.com/splicebox/MntJULiP#usage

When specifying --readLength, if your sample bam files don't have a fixed read length, you can just take the average of all of them and it will work well enough. Note that you will also probably need to use --variable-read-length in this case.