BPM - Bioinformatics Project Manager

A flexible, template-driven CLI tool for managing genomic projects. BPM helps you organize and manage your genomic analysis workflows with a consistent project structure and template-based approach.

Features

• Project initialization with standardized structure
• Template-based workflow management
• Support for demultiplexing, processing, and analysis workflows
• Project configuration management
• Command history tracking

Installation

From PyPI

pip install bpm

From Source

1. Clone the repository:

git clone https://github.com/ckuo/bpm.git
cd bpm

2. Install development dependencies:

pip install -e ".[dev]"

Usage

Initialize a New Project

bpm init --name 250704_ProjectA_ProjectB_MedI_3mRNAseq \
         --date 250704 \
         --institute MedI \
         --application 3mRNAseq \
         --authors "Chao-Chung Kuo <ckuo@ukaachen.de>" \
         --project-dir "nextgen2:/data/projects/250704_ProjectA_ProjectB_MedI_3mRNAseq"

Generate Workflow from Template

bpm generate bclconvert --raw nextgen:/novaseq/250704_A01742_0410_AHC3FFDRX5 \
                       --outdir nextgen:/data/fastq/250704

Update Project Configuration

bpm update demultiplexing.bclconvert.raw_data_path "nextgen:/novaseq/new_data"

Development

Running Tests

pytest

Code Style

# Format code
black .
isort .

# Type checking
mypy .

# Linting
ruff check .

License

This project is licensed under the MIT License - see the LICENSE file for details.