toil_example

A Command Line Interface created with cookiecutter-toil.

Usage

This package uses docker to manage its dependencies, there are 2 ways of using it:

1. Running the container in single machine mode without --batchSystem support:

    # using docker
    docker run -it papaemmelab/toil_example --help
   
    # using singularity
    singularity run docker://papaemmelab/toil_example --help
   

2. Installing the python package from pypi and passing the container as a flag:

    # install package
    pip install toil_example
   
    # run with docker
    toil_example [TOIL-OPTIONS] [PIPELINE-OPTIONS]
        --docker papaemmelab/toil_example
        --volumes <local path> <container path>
        --batchSystem LSF
   
    # run with singularity
    toil_example [TOIL-OPTIONS] [PIPELINE-OPTIONS]
        --singularity docker://papaemmelab/toil_example
        --volumes <local path> <container path>
        --batchSystem LSF
   

See docker2singularity if you want to use a singularity image instead of using the docker:// prefix.

Contributing

Contributions are welcome, and they are greatly appreciated, check our contributing guidelines!

Credits

This package was created using Cookiecutter and the papaemmelab/cookiecutter-toil project template.