Installation¶

This guide will help you install BPM and set up your environment for bioinformatics project management.

Prerequisites¶

Before installing BPM, ensure you have:

• Python 3.10 or higher installed on your system
• pip (Python package installer)
• Git (for repository management)

Check Your Python Version¶

python --version
# or
python3 --version

If you don't have Python 3.10+, you can download it from python.org.

Installation Methods¶

Method 1: Install from PyPI (Recommended)¶

The easiest way to install BPM is using pip:

pip install bpm

Method 2: Install from Source¶

If you want to install the latest development version:

# Clone the repository
git clone https://github.com/chaochungkuo/BPM.git
cd BPM

# Install in development mode
pip install -e .

Method 3: Using Conda (Coming Soon)¶

# This will be available once we publish to conda-forge
conda install -c conda-forge bpm

Verify Installation¶

After installation, verify that BPM is working correctly:

bpm --version

You should see output similar to:

BPM version 0.0.3

Configuration¶

Setting Up BPM Cache¶

BPM uses a cache directory to store repositories, templates, and other data. You need to set the BPM_CACHE environment variable:

Linux/macOS¶

Add this line to your shell configuration file (.bashrc, .zshrc, etc.):

export BPM_CACHE="/path/to/your/bpm_cache"

Then reload your shell configuration:

source ~/.bashrc
# or
source ~/.zshrc

Windows¶

Set the environment variable through System Properties or use:

setx BPM_CACHE "C:\path\to\your\bpm_cache"

Default Location¶

If you don't set BPM_CACHE, BPM will use the default location: - Linux/macOS: $HOME/.cache/bpm - Windows: %USERPROFILE%\.cache\bpm

Verify Configuration¶

Test that your cache directory is properly configured:

bpm info

This should show your BPM configuration including the cache directory.

Dependencies¶

BPM automatically installs the following dependencies:

• pydantic (≥2.0.0) - Data validation
• pyyaml (≥6.0.0) - YAML file handling
• typer (≥0.9.0) - CLI framework
• rich (≥13.0.0) - Terminal formatting
• jinja2 (≥3.1.0) - Template engine
• ruamel.yaml (≥0.17.0) - YAML processing
• psutil (≥6.0.0) - System utilities
• httpx (≥0.24.0) - HTTP client
• gitpython (≥3.1.0) - Git integration

Troubleshooting¶

Common Installation Issues¶

Permission Errors¶

If you encounter permission errors during installation:

# Use user installation
pip install --user bpm

# Or use a virtual environment
python -m venv bpm_env
source bpm_env/bin/activate  # On Windows: bpm_env\Scripts\activate
pip install bpm

Python Version Issues¶

Ensure you're using Python 3.10 or higher:

# Check Python version
python --version

# If you have multiple Python versions, use python3
python3 --version

Cache Directory Issues¶

If BPM can't access the cache directory:

# Create the directory manually
mkdir -p /path/to/your/bpm_cache

# Set proper permissions
chmod 755 /path/to/your/bpm_cache

Getting Help¶

If you encounter issues during installation:

1. Check the Common Issues page
2. Look at the FAQ
3. Open an issue on GitHub

Next Steps¶

Once BPM is installed and configured, you can:

1. Quick Start Guide - Get your first project running
2. Configuration - Learn about advanced configuration options
3. User Guide - Explore BPM's features

Updating BPM¶

To update BPM to the latest version:

pip install --upgrade bpm

To check for updates:

pip list --outdated | grep bpm