Quickstart

Prerequisities

The preferred way of running mitopy is through Docker. Please install Docker and Docker Compose on your system.

Run mitopy

Clone the repository:

git clone https://github.com/bendda/mitopy

Start the Docker container in interactive mode:

cd mitopy
docker compose run mitopy

Run the whole mitopy pipeline on example data:

mitopy run-pipeline example_data/NA12878_20k_hg38.bam -o example_data/outputs

To run the analysis on your files, please add them to data/ directory.

Note

It is important to add custom data required for analysis to data/ directory, since the data/ directory is mounted to Docker container (for further information, see Docker Volumes).

Run tests

To run a suite of mitopy tests, run following command (in the cloned mitopy directory):

docker compose run test