--- a/COBRAxy/docs/installation.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/installation.md	Sun Oct 26 19:27:41 2025 +0000
@@ -4,38 +4,70 @@
 
 ## System Requirements
 
-- **Python**: 3.8-3.12
+- **Python**: 3.8-3.13
 - **Operating System**: Linux (recommended), macOS, Windows
-- **Storage**: 2GB free space for installation and temporary files
+- **Build tools**: C/C++ compiler (gcc, clang, or MSVC), CMake, pkg-config
+
+## System Dependencies
+
+Install required build tools before installing COBRAxy:
+
+```bash
+# Ubuntu/Debian
+sudo apt-get install build-essential cmake pkg-config libvips libglpk40 glpk-utils
+
+# macOS
+xcode-select --install
+brew install cmake pkg-config vips glpk
+
+# Windows (with Chocolatey)
+choco install cmake visualstudio2022buildtools pkgconfiglite
+```
+
+## Installation Methods
 
-## Quick Install
+### Recommended: Using Conda
+
+Create an isolated environment with all dependencies:
+
+```bash
+# Create a new conda environment
+conda create -n cobraxy python=3.13 -y
+conda activate cobraxy
 
-The fastest way to install COBRAxy:
+# Install build tools via conda
+conda install -c conda-forge cmake pkg-config swiglpk -y
+
+# Clone and install COBRAxy
+git clone https://github.com/CompBtBs/COBRAxy.git
+cd COBRAxy/src
+pip install .
+```
+
+### Alternative: Direct Installation
+
+If you have system dependencies already installed:
 
 ```bash
 # Clone the repository
 git clone https://github.com/CompBtBs/COBRAxy.git
-cd COBRAxy
+cd COBRAxy/src
 
 # Install COBRAxy
 pip install .
 ```
 
-## Development Install
+### Development Install
 
 For development or if you want to modify COBRAxy:
 
 ```bash
-# Clone and install in development mode
+# Clone and install in editable mode
 git clone https://github.com/CompBtBs/COBRAxy.git
-cd COBRAxy
+cd COBRAxy/src
 pip install -e .
 ```
 
-## Dependencies
-
-COBRAxy automatically installs its Python dependencies (COBRApy, pandas, numpy, etc.)
-
 ## Verify Installation
 
 Test your installation:
@@ -44,9 +76,53 @@
 # Check if COBRAxy tools are available
 ras_generator --help
 flux_simulation --help
+marea --help
+
+# Check Python can import COBRAxy modules
+python -c "import ras_generator; print('COBRAxy installed successfully!')"
+```
+
+## Troubleshooting Installation
+
+### Missing Compiler Errors
+
+If you see errors about missing compilers during installation:
+
+```bash
+# Ubuntu/Debian
+sudo apt-get install build-essential
+
+# macOS
+xcode-select --install
 ```
 
-## Virtual Environment (Recommended)
+### CMake Not Found
+
+```bash
+# Ubuntu/Debian
+sudo apt-get install cmake
+
+# macOS
+brew install cmake
+
+# Or via conda
+conda install -c conda-forge cmake
+```
+
+### pkg-config Issues
+
+```bash
+# Ubuntu/Debian
+sudo apt-get install pkg-config
+
+# macOS
+brew install pkg-config
+
+# Or via conda
+conda install -c conda-forge pkg-config
+```
+
+## Alternative: Virtual Environment (without Conda)
 
 Using a virtual environment prevents conflicts with other Python packages:
 
@@ -59,6 +135,7 @@
 # cobraxy-env\Scripts\activate  # Windows
 
 # Install COBRAxy
+cd COBRAxy/src
 pip install .
 
 # When done, deactivate
@@ -69,15 +146,14 @@
 
 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
+1. **[Quick Start Guide](/quickstart.md)** - Run your first analysis
+2. **[Tutorial: Galaxy Setup](/tutorials/galaxy-setup.md)** - Set up web interface
 
 ## Getting Help
 
 If you encounter issues:
 
-1. Check the [Troubleshooting Guide](troubleshooting.md)
+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