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REPRODUCING.md

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REPRODUCING.md

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This Code Ocean Compute Capsule will allow you to run and reproduce the results of Pre-Mutect2 on your local machine1. Follow the instructions below, or consult our knowledge base for more information. Don't hesitate to reach out via live chat or email if you have any questions.

1 You may need access to additional hardware and/or software licenses.

Prerequisites

Instructions

Download attached Data Assets

In order to fetch the Data Asset(s) this Capsule depends on, download them into the Capsule's data folder:

Log in to the Docker registry

In your terminal, execute the following command, providing your password or API key when prompted for it:

docker login -u stephen@codeocean.com registry.apps.codeocean.com

Run the Capsule to reproduce the results

In your terminal, navigate to the folder where you've extracted the Capsule and execute the following command, adjusting parameters as needed:

docker run --platform linux/amd64 --rm \
  --workdir /code \
  --volume "$PWD/code":/code \
  --volume "$PWD/data":/data \
  --volume "$PWD/results":/results \
  registry.apps.codeocean.com/capsule/f70cf89d-0417-49cb-ba68-4aba404d1998 \
  bash run