toil_pindel
A toil wrapper for cgp pindel.
Usage
This package uses docker to manage its dependencies, there are 2 ways of using it:
-
Running the container in single machine mode without
--batchSystem
support:# using docker docker run -it papaemmelab/toil_pindel --help # using singularity singularity run docker://papaemmelab/toil_pindel --help
-
Installing the python package from pypi and passing the container as a flag:
# install package pip install toil_pindel # run with docker toil_pindel [TOIL-OPTIONS] [PIPELINE-OPTIONS] --docker papaemmelab/toil_pindel --volumes <local path> <container path> --batchSystem LSF # run with singularity toil_pindel [TOIL-OPTIONS] [PIPELINE-OPTIONS] --singularity docker://papaemmelab/toil_pindel --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.