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Installation

You don't have to build a local environment for running Shiba! We provide a Docker image of Shiba, which includes all the dependencies and the Shiba software itself. You can run them using Docker/Singularity or Snakemake.

Docker

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# Pull the latest image
docker pull naotokubota/shiba:latest

# Login to the container
docker run -it --rm naotokubota/shiba:latest bash

# Run Shiba, for example, to see the help message
docker run -it --rm naotokubota/shiba:latest python /opt_shiba/Shiba/shiba.py -h

Singularity

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# Pull the latest image
singularity pull docker://naotokubota/shiba:latest

# Login to the container
singularity shell shiba_latest.sif

# Run Shiba, for example, to see the help message
singularity exec shiba_latest.sif python /opt_shiba/Shiba/shiba.py -h

Snakemake

You need to install Snakemake and clone the Shiba GitHub repository on your system:

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# Clone the Shiba repository
git clone https://github.com/NaotoKubota/Shiba.git

And please make sure you have Singularity installed on your system as the snakemake workflow uses Singularity to run each step of the pipeline.