Metadata-Version: 2.4
Name: bio_pype
Version: 2.0.99rc8
Summary: Management and development framework for bioinformatics pipelines
Author-email: Francesco Favero <favero.francesco@gmail.com>
License-Expression: MIT
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Information Technology
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Application Frameworks
Classifier: Topic :: System :: Distributed Computing
Classifier: Topic :: Utilities
Requires-Python: >=3.4
Description-Content-Type: text/x-rst
License-File: LICENSE.txt
Requires-Dist: PyYAML
Requires-Dist: psutil
Requires-Dist: rich
Requires-Dist: semantic-version>=2.10.0
Requires-Dist: pygls<2.0,>=1.3.0
Requires-Dist: nvidia-ml-py>=13.590.48
Provides-Extra: test
Requires-Dist: pytest>=7.0; extra == "test"
Requires-Dist: pytest-cov>=4.0; extra == "test"
Provides-Extra: docs
Requires-Dist: sphinx>=4.0; extra == "docs"
Requires-Dist: sphinx-rtd-theme>=1.0; extra == "docs"
Requires-Dist: sphinxcontrib-programoutput; extra == "docs"
Requires-Dist: myst-parser>=1.0.0; extra == "docs"
Dynamic: license-file

BIO pype
========

A Python Framework for Bioinformatics Pipeline Management
------------------------------------------------------------

Bio_pype provides a comprehensive framework for building, organizing, and standardizing
bioinformatics tools and pipelines. Built on Python's robust argparse_ module, it offers
both command-line accessibility and programmatic flexibility.

Key Features
------------

- Modular pipeline construction
- Environment management integration (Environment Modules_, Docker_, Conda_, etc.)
- Multiple queue system support (MOAB_Torque_, SLURM_, etc.)
- Version-controlled configurations
- Reproducible execution environments

Installation
------------

**From PyPI**

::

    pip install bio-pype

**Development Version**

::

    git clone https://codeberg.org/bio-pype/bio-pype
    cd bio-pype
    python setup.py test
    python setup.py install

Basic Usage
-----------

Available Commands::

    $ pype --help
    usage: pype [-p PROFILE]
                {compute_bio,pipelines,profiles,registry,resume,run,snippets,validate}
                ...

    A python pipeliens manager oriented for bioinformatics

    positional arguments:

    Simplified:
    run            Run pipelines using simplified template-
                    based interface

    Run:
    pipelines      Run pipelines with queue system integration
    resume         Resume pipeline execution from runtime YAML with
                    environment restoration
    snippets       Run individual tasks as snippets

    Manage:
    profiles       Configure and validate execution environments
    registry       Workflow manager for bio-pype

    Diagnostics:
    validate       Validate bio_pype modules for correctness and
                    compatibility

    API Integration:
    compute_bio    Test compute.bio credentials and run persistent listener
                    daemon

    options:
    -p PROFILE, --profile PROFILE
                        Choose the pype profile from the available options (see
                        pype profiles). Default: None

    This is version 2.0.99rc2 - Francesco Favero - 29 Janury 2026


Advanced Configuration
----------------------

Environment variables allow custom module locations::

    # Use local snippets
    export PYPE_SNIPPETS=path/to/snippets
    pype snippets

    # Use local pipelines
    export PYPE_PIPELINES=path/to/pipelines
    pype pipelines

For complete documentation, visit our `Read the Docs`_ site.

.. _argparse: https://docs.python.org/3/library/argparse.html
.. _Modules: http://modules.sourceforge.net
.. _Docker: https://www.docker.com
.. _Conda: https://anaconda.org
.. _MOAB_Torque: http://www.adaptivecomputing.com
.. _SLURM: https://slurm.schedmd.com
.. _Read the Docs: http://bio-pype.readthedocs.io
