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

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date Tue, 28 Oct 2025 10:44:07 +0000
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5 ## System Requirements 5 ## System Requirements
6 6
7 - **Python**: 3.8-3.13 7 - **Python**: 3.8-3.13
8 - **Operating System**: Linux (recommended), macOS, Windows 8 - **Operating System**: Linux (recommended), macOS, Windows
9 - **Build tools**: C/C++ compiler (gcc, clang, or MSVC), CMake, pkg-config 9 - **Build tools**: C/C++ compiler (gcc, clang, or MSVC), CMake, pkg-config
10
11 ## System Dependencies
12
13 Install required build tools before installing COBRAxy:
14
15 ```bash
16 # Ubuntu/Debian
17 sudo apt-get install build-essential cmake pkg-config libvips libglpk40 glpk-utils
18
19 # macOS
20 xcode-select --install
21 brew install cmake pkg-config vips glpk
22
23 # Windows (with Chocolatey)
24 choco install cmake visualstudio2022buildtools pkgconfiglite
25 ```
26 10
27 ## Installation Methods 11 ## Installation Methods
28 12
29 ### Recommended: Using Conda 13 ### Recommended: Using Conda
30 14
42 git clone https://github.com/CompBtBs/COBRAxy.git 26 git clone https://github.com/CompBtBs/COBRAxy.git
43 cd COBRAxy/src 27 cd COBRAxy/src
44 pip install . 28 pip install .
45 ``` 29 ```
46 30
47 ### Alternative: Direct Installation
48
49 If you have system dependencies already installed:
50
51 ```bash
52 # Clone the repository
53 git clone https://github.com/CompBtBs/COBRAxy.git
54 cd COBRAxy/src
55
56 # Install COBRAxy
57 pip install .
58 ```
59
60 ### Development Install
61
62 For development or if you want to modify COBRAxy:
63
64 ```bash
65 # Clone and install in editable mode
66 git clone https://github.com/CompBtBs/COBRAxy.git
67 cd COBRAxy/src
68 pip install -e .
69 ```
70 31
71 ## Verify Installation 32 ## Verify Installation
72 33
73 Test your installation: 34 Test your installation:
74 35
144 105
145 ## Next Steps 106 ## Next Steps
146 107
147 After successful installation: 108 After successful installation:
148 109
149 1. **[Quick Start Guide](/quickstart.md)** - Run your first analysis 110 1. **[Quick Start Guide](quickstart)** - Run your first analysis
150 2. **[Tutorial: Galaxy Setup](/tutorials/galaxy-setup.md)** - Set up web interface 111 2. **[Tutorial: Galaxy Setup](tutorials/galaxy-setup)** - Set up web interface
151 112
152 ## Getting Help 113 ## Getting Help
153 114
154 If you encounter issues: 115 If you encounter issues:
155 116
156 1. Check the [Troubleshooting Guide](/troubleshooting.md) 117 1. Check the [Troubleshooting Guide](troubleshooting)
157 2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues) 118 2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues)
158 3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with: 119 3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with:
159 - Your operating system 120 - Your operating system
160 - Python version (`python --version`) 121 - Python version (`python --version`)
161 - Complete error message 122 - Complete error message