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Usage via Docker
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**Download "data_dir" from GitHub, the folder is needed as an input argument.**

Be sure you have Docker `installed <https://www.docker.com/products/docker-desktop>`_ on your machine. No Docker account is needed. 
Do the following to pull the image locally:

::

	docker pull kvdlab/puma:1.2.1

Now you should be able to run the image and see the following output:

::

	$ docker run --rm -it kvdlab/puma:1.2.1
	usage: run_puma.py [-h] -i FILE [-f FORMAT] [-d DIR] [-o DIR] [-e FLOAT]
	[-m NUM] [-D STR] [-L FILE]
	run_puma.py: error: the following arguments are required: -i/--input

To run Puma on your data, you will need to `mount <https://docs.docker.com/storage/bind-mounts/>`_ your local input and output direc:xtories.
For instance, from within this "docker" directory, we can run the program like so:

::

	$ docker run --rm \
	-v `pwd`/../data_dir:/data \           <1>
	-v `pwd`/../input_and_output:/in_out \ <2>
	kvdlab/puma:1.2.1 \                    <3>
	run_puma.py -i /in_out/BPV2_new.fa -o /in_out/puma_out -d /data <4>

1. The "data_dir" dir will be mounted as "/data"
2. The "input_and_output" dir will be mounted as "/in_out"
3. This is the tag of the Docker image to run
4. This is the command to execute Puma with the input and output arguments

**Be sure to avoid using a space before or after the colon when mounting the directories using the "-v" argument.**

**When running PuMA through Docker, the output argument needs to be specified ('-o'). In the above example the "input_and_output" folder represents where the input file and the "puma_out" directory are. The output directory is "puma_out" since part of the command is "-o /in_out/puma_out". For ease of use, it is recommended that there is one folder for the input and output like the above example**

**Once PuMA executes, the output folder will be in the specified local directory. For the above example, the "puma_out" folder will be in the directory "input_and_output".**