diff COBRAxy/docs/installation.md @ 547:73f2f7e2be17 draft

Uploaded

--- a/COBRAxy/docs/installation.md	Mon Oct 27 12:33:08 2025 +0000
+++ b/COBRAxy/docs/installation.md	Tue Oct 28 10:44:07 2025 +0000
@@ -8,22 +8,6 @@
 - **Operating System**: Linux (recommended), macOS, Windows
 - **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
 
 ### Recommended: Using Conda
@@ -44,29 +28,6 @@
 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/src
-
-# Install COBRAxy
-pip install .
-```
-
-### Development Install
-
-For development or if you want to modify COBRAxy:
-
-```bash
-# Clone and install in editable mode
-git clone https://github.com/CompBtBs/COBRAxy.git
-cd COBRAxy/src
-pip install -e .
-```
 
 ## Verify Installation
 
@@ -146,17 +107,17 @@
 
 After successful installation:
 
-1. **[Quick Start Guide](/quickstart.md)** - Run your first analysis
-2. **[Tutorial: Galaxy Setup](/tutorials/galaxy-setup.md)** - Set up web interface
+1. **[Quick Start Guide](quickstart)** - Run your first analysis
+2. **[Tutorial: Galaxy Setup](tutorials/galaxy-setup)** - Set up web interface
 
 ## Getting Help
 
 If you encounter issues:
 
-1. Check the [Troubleshooting Guide](/troubleshooting.md)
+1. Check the [Troubleshooting Guide](troubleshooting)
 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
\ No newline at end of file
+   - Installation method used