leukgen/register_toil repository overview

⁠register_toil

👾 Register versioned toil container⁠ pipelines or other commands in singularity containers.

⁠Installation

This package is available at PyPi⁠:

pip install register_toil

⚠️ WARNING: This package only works with singularity 2.4+

⁠Usage

register_toil will install toil container⁠ pipelines in separate virtual environments⁠, pull a singularity image from the dockerhub and create executables that call the pipeline with the right parameters:

register_toil \
    --bindir /example/bin \
    --optdir /example/opt \
    --tmpvar $TMP \
    --pypi_name toil_disambiguate \
    --pypi_version v0.1.2 \
    --volumes /ifs /ifs

Given this call, the following directory structure is created:

/example/
├── bin
│   └── toil_disambiguate_v0.1.2 -> /example/opt/toil_disambiguate/v0.1.2/toil_disambiguate
└── opt
    └── toil_disambiguate
        └── v0.1.2
            ├── toil_disambiguate
            └── toil_disambiguate-v0.1.2.simg

And the executables look like this:

cat /example/bin/toil_disambiguate
#!/bin/bash
/path/to/.virtualenvs/production__toil_disambiguate__v0.1.2/bin/toil_disambiguate $@ \
    --singularity /example/opt/toil_disambiguate/v0.1.2/toil_disambiguate-v0.1.2.simg \
    --volumes /ifs /ifs \
    --workDir $TMP_DIR

Similar usage is provided to register regular commands that will run inside a container, see register_singularity.

⁠Contributing

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

⁠Credits

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