Added Docker build and setup instructions

Bacteria methylate their DNA in three ways: 6-methyladenine (6mA), 5-methylcytosine (5mC), and 4-methylcytosine (4mC). While historically most sequencing technologies could only practially detect up to two of the three types of modifications, nanopore sequencers have shown they can detect all three modifications from the same dataset at a less expensive cost than other sequencing methods. While some tools exist to analyse these data to make methylation motif calls (aka "discover the methylome"), we wrote MIJAMP (MIJAMP Is Just A MethylBED Parser) because we wanted less of an automated pipeline with no human intervention necessary (or possible, in many cases) and more of a workflow consisting of a robust set of tools developed to assist humans in analyzing genome-scale datasets.

## Installation

Before running MIJAMP for the first time, ensure that all dependencies have been installed. MIJAMP requires [MEME](https://meme-suite.org/meme/doc/download.html), [Modkit](https://github.com/nanoporetech/modkit), [Minimap2](https://github.com/lh3/minimap2), and [SAMtools](http://www.htslib.org/download/) to be present in your system's PATH, while the Python packages [Pandas](https://pypi.org/project/pandas/), [Biopython](https://pypi.org/project/biopython/), and [Xmltodict](https://pypi.org/project/xmltodict/) are also required. Additionally, [Dorado](https://github.com/nanoporetech/doradofil) and [Filtlong](https://github.com/rrwick/Filtlong) are highly recommended. 

MIJAMP requires [MEME](https://meme-suite.org/meme/doc/download.html), [Modkit](https://github.com/nanoporetech/modkit), [Minimap2](https://github.com/lh3/minimap2), and [SAMtools](http://www.htslib.org/download/) to be present in your system's PATH, while the Python packages [Pandas](https://pypi.org/project/pandas/), [Biopython](https://pypi.org/project/biopython/), and [Xmltodict](https://pypi.org/project/xmltodict/) are also required. 

Once dependencies are installed, download and uncompress the repository, then make all Python scripts executable.

To expedite installation, a dockerfile is provided to build a Docker image. First, download and decompress the MIJAMP repository.

```

$ wget https://code.ornl.gov/alexander-public/mijamp/-/archive/main/mijamp-main.zip`

$ unzip mijamp-main.zip

$ wget https://code.ornl.gov/alexander-public/mijamp/-/archive/main/mijamp-main.tar.gz

$ tar xvf mijamp-main.tar.gz

$ cd mijamp-main

$ chmod u+x *.py

```

MIJAMP is now ready to discover methylomes.

Once in the mijamp-main directory build the MIJAMP image, then run the container in interactive mode, naming it mijamp:

```

$ sudo docker build -t mijamp .

$ sudo docker run --name mijamp -it mijamp

```

You should now have a prompt within the container. Complete setting up the container with:

```

# setupScript

```

Confirm successful installation by running through the Quick Start Guide using the _E. coli_ data. Once successful installation has been confirmed, commit changes to the container by entering the following command in a new terminal window.

```

$ sudo docker commit mijamp

```

## Quick Start Guide Using Test Data

The MIJAMP repository contains data from _Escherichia coli_ K12 MG1655 and _Picosynecococcus sp._ PCC7002 that serves as test and training data for users. Each folder contains a genome sequence and a BAM file containing 100x coverage worth of reads that have been called to detect DNA modifications, so these data are ready for preprocessing. Note that # below should be replaced with the number of threads you wish to use during preprocessing (more is definitely better).