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1 # Installation
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2
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3 This guide walks you through installing COBRAxy on your system.
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4
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5 ## System Requirements
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6
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7 - **Python**: 3.8-3.13
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8 - **Operating System**: Linux (recommended), macOS, Windows
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9 - **Build tools**: C/C++ compiler (gcc, clang, or MSVC), CMake, pkg-config
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10
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11 ## Installation Methods
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12
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13 ### Recommended: Using Conda
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14
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15 Create an isolated environment with all dependencies:
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16
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17 ```bash
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18 # Create a new conda environment
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19 conda create -n cobraxy python=3.13 -y
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20 conda activate cobraxy
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21
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22 # Install build tools via conda
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23 conda install -c conda-forge cmake pkg-config swiglpk -y
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24
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25 # Clone and install COBRAxy
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26 git clone https://github.com/CompBtBs/COBRAxy.git
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27 cd COBRAxy/src
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28 pip install .
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29 ```
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30
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31
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32 ## Verify Installation
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33
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34 Test your installation:
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35
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36 ```bash
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37 # Check if COBRAxy tools are available
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38 ras_generator --help
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39 flux_simulation --help
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40 marea --help
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41
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42 # Check Python can import COBRAxy modules
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43 python -c "import ras_generator; print('COBRAxy installed successfully!')"
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44 ```
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45
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46 ## Troubleshooting Installation
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47
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48 ### Missing Compiler Errors
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49
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50 If you see errors about missing compilers during installation:
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51
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52 ```bash
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53 # Ubuntu/Debian
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54 sudo apt-get install build-essential
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55
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56 # macOS
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57 xcode-select --install
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58 ```
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59
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60 ### CMake Not Found
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61
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62 ```bash
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63 # Ubuntu/Debian
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64 sudo apt-get install cmake
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65
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66 # macOS
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67 brew install cmake
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68
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69 # Or via conda
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70 conda install -c conda-forge cmake
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71 ```
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72
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73 ### pkg-config Issues
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74
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75 ```bash
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76 # Ubuntu/Debian
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77 sudo apt-get install pkg-config
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78
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79 # macOS
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80 brew install pkg-config
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81
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82 # Or via conda
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83 conda install -c conda-forge pkg-config
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84 ```
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85
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86 ## Alternative: Virtual Environment (without Conda)
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87
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88 Using a virtual environment prevents conflicts with other Python packages:
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89
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90 ```bash
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91 # Create virtual environment
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92 python -m venv cobraxy-env
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93
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94 # Activate environment
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95 source cobraxy-env/bin/activate # Linux/macOS
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96 # cobraxy-env\Scripts\activate # Windows
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97
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98 # Install COBRAxy
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99 cd COBRAxy/src
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100 pip install .
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101
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102 # When done, deactivate
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103 deactivate
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104 ```
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105
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106 ## Next Steps
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107
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108 After successful installation:
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109
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110 1. **[Quick Start Guide](quickstart)** - Run your first analysis
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111 2. **[Tutorial: Galaxy Setup](tutorials/galaxy-setup)** - Set up web interface
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112
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113 ## Getting Help
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114
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115 If you encounter issues:
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116
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117 1. Check the [Troubleshooting Guide](troubleshooting)
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118 2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues)
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119 3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with:
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120 - Your operating system
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121 - Python version (`python --version`)
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122 - Complete error message
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123 - Installation method used
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