condathis: Run Any CLI Tool in a 'Conda' Environment

Runs command line interface (CLI) tools in isolated and reproducible 'Conda' environments from R. Environments are created and managed with 'micromamba' https://mamba.readthedocs.io/en/latest/, which is downloaded when no usable copy is found. Commands run with their environment activated, alone or as pipelines connected by pipes, and other packages can add backends that create and run environments.

Details

Create an environment with create_env(). Run a command line tool in it with run(), or run several tools connected by pipes with run_pipeline(). Read the output with parse_output(). Start with vignette("condathis"). condathis-options lists the options and environment variables that condathis reads. condathis-conditions lists the classes of its errors and warnings.

See also

Useful links:

• https://github.com/luciorq/condathis

• https://luciorq.github.io/condathis/

• Report bugs at https://github.com/luciorq/condathis/issues

Author

Maintainer: Lucio Queiroz luciorqueiroz@gmail.com (ORCID) [copyright holder]

Authors:

• Lucio Queiroz luciorqueiroz@gmail.com (ORCID) [copyright holder]

• Claudio Zanettini claudio.zanettini@gmail.com (ORCID) [contributor]