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+# Installation
+
+This guide walks you through installing COBRAxy on your system.
+
+## System Requirements
+
+- **Python**: 3.8-3.11
+- **Operating System**: Linux (recommended), macOS, Windows
+- **Storage**: 2GB free space for installation and temporary files
+
+## Quick Install
+
+The fastest way to install COBRAxy:
+
+```bash
+# Clone the repository
+git clone https://github.com/CompBtBs/COBRAxy.git
+cd COBRAxy
+
+# Install COBRAxy
+pip install .
+```
+
+## Development Install
+
+For development or if you want to modify COBRAxy:
+
+```bash
+# Clone and install in development mode
+git clone https://github.com/CompBtBs/COBRAxy.git
+cd COBRAxy
+pip install -e .
+```
+
+## Dependencies
+
+COBRAxy automatically installs its Python dependencies:
+
+- **COBRApy** - Core metabolic modeling
+- **pandas** - Data manipulation
+- **numpy** - Numerical computations
+- **scipy** - Scientific computing
+
+## Optional System Libraries
+
+Install additional libraries for enhanced features:
+
+### Ubuntu/Debian
+
+```bash
+# Install GLPK solver
+sudo apt-get update
+sudo apt-get install libglpk40 glpk-utils
+
+# Install libvips for SVG processing
+sudo apt-get install libvips
+
+# Install Python GLPK bindings
+pip install swiglpk
+```
+
+### macOS
+
+```bash
+# Using Homebrew
+brew install glpk vips
+
+# Install Python bindings
+pip install swiglpk
+```
+
+### Windows
+
+```bash
+# Using conda (recommended for Windows)
+conda install -c conda-forge glpk
+
+# Or using pip
+pip install swiglpk
+```
+
+## Verify Installation
+
+Test your installation:
+
+```bash
+# Check if COBRAxy tools are available
+ras_generator --help
+flux_simulation --help
+
+# Test with example data (if available)
+cd COBRAxy
+python testing.py
+```
+
+## Troubleshooting Installation
+
+### Common Issues
+
+**Import Error: No module named 'cobra'**
+```bash
+# Install COBRApy manually
+pip install cobra
+```
+
+**GLPK solver not found**
+```bash
+# Install GLPK solver
+# Ubuntu/Debian: sudo apt-get install glpk-utils
+# macOS: brew install glpk
+# Then: pip install swiglpk
+```
+
+**Permission denied errors**
+```bash
+# Use user installation
+pip install --user .
+# Or use virtual environment (recommended)
+python -m venv cobraxy-env
+source cobraxy-env/bin/activate  # Linux/macOS
+# cobraxy-env\Scripts\activate  # Windows
+pip install .
+```
+
+## Virtual Environment (Recommended)
+
+Using a virtual environment prevents conflicts with other Python packages:
+
+```bash
+# Create virtual environment
+python -m venv cobraxy-env
+
+# Activate environment
+source cobraxy-env/bin/activate  # Linux/macOS
+# cobraxy-env\Scripts\activate  # Windows
+
+# Install COBRAxy
+pip install .
+
+# When done, deactivate
+deactivate
+```
+
+## Next Steps
+
+After successful installation:
+
+1. **[Quick Start Guide](quickstart.md)** - Run your first analysis
+2. **[Tutorial: Python API](tutorials/python-api.md)** - Learn programmatic usage
+3. **[Tutorial: Galaxy Setup](tutorials/galaxy-setup.md)** - Set up web interface
+
+## Getting Help
+
+If you encounter issues:
+
+1. Check the [Troubleshooting Guide](troubleshooting.md)
+2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues)
+3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with:
+   - Your operating system
+   - Python version (`python --version`)
+   - Complete error message
+   - Installation method used
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