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.