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2 2
3 This guide walks you through installing COBRAxy on your system. 3 This guide walks you through installing COBRAxy on your system.
4 4
5 ## System Requirements 5 ## System Requirements
6 6
7 - **Python**: 3.8-3.12 7 - **Python**: 3.8-3.13
8 - **Operating System**: Linux (recommended), macOS, Windows 8 - **Operating System**: Linux (recommended), macOS, Windows
9 - **Storage**: 2GB free space for installation and temporary files 9 - **Build tools**: C/C++ compiler (gcc, clang, or MSVC), CMake, pkg-config
10 10
11 ## Quick Install 11 ## System Dependencies
12 12
13 The fastest way to install COBRAxy: 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
27 ## Installation Methods
28
29 ### Recommended: Using Conda
30
31 Create an isolated environment with all dependencies:
32
33 ```bash
34 # Create a new conda environment
35 conda create -n cobraxy python=3.13 -y
36 conda activate cobraxy
37
38 # Install build tools via conda
39 conda install -c conda-forge cmake pkg-config swiglpk -y
40
41 # Clone and install COBRAxy
42 git clone https://github.com/CompBtBs/COBRAxy.git
43 cd COBRAxy/src
44 pip install .
45 ```
46
47 ### Alternative: Direct Installation
48
49 If you have system dependencies already installed:
14 50
15 ```bash 51 ```bash
16 # Clone the repository 52 # Clone the repository
17 git clone https://github.com/CompBtBs/COBRAxy.git 53 git clone https://github.com/CompBtBs/COBRAxy.git
18 cd COBRAxy 54 cd COBRAxy/src
19 55
20 # Install COBRAxy 56 # Install COBRAxy
21 pip install . 57 pip install .
22 ``` 58 ```
23 59
24 ## Development Install 60 ### Development Install
25 61
26 For development or if you want to modify COBRAxy: 62 For development or if you want to modify COBRAxy:
27 63
28 ```bash 64 ```bash
29 # Clone and install in development mode 65 # Clone and install in editable mode
30 git clone https://github.com/CompBtBs/COBRAxy.git 66 git clone https://github.com/CompBtBs/COBRAxy.git
31 cd COBRAxy 67 cd COBRAxy/src
32 pip install -e . 68 pip install -e .
33 ``` 69 ```
34
35 ## Dependencies
36
37 COBRAxy automatically installs its Python dependencies (COBRApy, pandas, numpy, etc.)
38 70
39 ## Verify Installation 71 ## Verify Installation
40 72
41 Test your installation: 73 Test your installation:
42 74
43 ```bash 75 ```bash
44 # Check if COBRAxy tools are available 76 # Check if COBRAxy tools are available
45 ras_generator --help 77 ras_generator --help
46 flux_simulation --help 78 flux_simulation --help
79 marea --help
80
81 # Check Python can import COBRAxy modules
82 python -c "import ras_generator; print('COBRAxy installed successfully!')"
47 ``` 83 ```
48 84
49 ## Virtual Environment (Recommended) 85 ## Troubleshooting Installation
86
87 ### Missing Compiler Errors
88
89 If you see errors about missing compilers during installation:
90
91 ```bash
92 # Ubuntu/Debian
93 sudo apt-get install build-essential
94
95 # macOS
96 xcode-select --install
97 ```
98
99 ### CMake Not Found
100
101 ```bash
102 # Ubuntu/Debian
103 sudo apt-get install cmake
104
105 # macOS
106 brew install cmake
107
108 # Or via conda
109 conda install -c conda-forge cmake
110 ```
111
112 ### pkg-config Issues
113
114 ```bash
115 # Ubuntu/Debian
116 sudo apt-get install pkg-config
117
118 # macOS
119 brew install pkg-config
120
121 # Or via conda
122 conda install -c conda-forge pkg-config
123 ```
124
125 ## Alternative: Virtual Environment (without Conda)
50 126
51 Using a virtual environment prevents conflicts with other Python packages: 127 Using a virtual environment prevents conflicts with other Python packages:
52 128
53 ```bash 129 ```bash
54 # Create virtual environment 130 # Create virtual environment
57 # Activate environment 133 # Activate environment
58 source cobraxy-env/bin/activate # Linux/macOS 134 source cobraxy-env/bin/activate # Linux/macOS
59 # cobraxy-env\Scripts\activate # Windows 135 # cobraxy-env\Scripts\activate # Windows
60 136
61 # Install COBRAxy 137 # Install COBRAxy
138 cd COBRAxy/src
62 pip install . 139 pip install .
63 140
64 # When done, deactivate 141 # When done, deactivate
65 deactivate 142 deactivate
66 ``` 143 ```
67 144
68 ## Next Steps 145 ## Next Steps
69 146
70 After successful installation: 147 After successful installation:
71 148
72 1. **[Quick Start Guide](quickstart.md)** - Run your first analysis 149 1. **[Quick Start Guide](/quickstart.md)** - Run your first analysis
73 2. **[Tutorial: Python API](tutorials/python-api.md)** - Learn programmatic usage 150 2. **[Tutorial: Galaxy Setup](/tutorials/galaxy-setup.md)** - Set up web interface
74 3. **[Tutorial: Galaxy Setup](tutorials/galaxy-setup.md)** - Set up web interface
75 151
76 ## Getting Help 152 ## Getting Help
77 153
78 If you encounter issues: 154 If you encounter issues:
79 155
80 1. Check the [Troubleshooting Guide](troubleshooting.md) 156 1. Check the [Troubleshooting Guide](/troubleshooting.md)
81 2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues) 157 2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues)
82 3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with: 158 3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with:
83 - Your operating system 159 - Your operating system
84 - Python version (`python --version`) 160 - Python version (`python --version`)
85 - Complete error message 161 - Complete error message