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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**: 3.8-3.11
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8 - **Operating System**: Linux (recommended), macOS, Windows
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9 - **Storage**: 2GB free space for installation and temporary files
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10
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11 ## Quick Install
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12
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13 The fastest way to install COBRAxy:
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14
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15 ```bash
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16 # Clone the repository
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17 git clone https://github.com/CompBtBs/COBRAxy.git
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18 cd COBRAxy
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19
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20 # Install COBRAxy
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21 pip install .
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22 ```
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23
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24 ## Development Install
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25
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26 For development or if you want to modify COBRAxy:
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27
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28 ```bash
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29 # Clone and install in development mode
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30 git clone https://github.com/CompBtBs/COBRAxy.git
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31 cd COBRAxy
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32 pip install -e .
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33 ```
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34
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35 ## Dependencies
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36
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37 COBRAxy automatically installs its Python dependencies:
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38
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39 - **COBRApy** - Core metabolic modeling
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40 - **pandas** - Data manipulation
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41 - **numpy** - Numerical computations
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42 - **scipy** - Scientific computing
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43
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44 ## Optional System Libraries
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45
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46 Install additional libraries for enhanced features:
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47
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48 ### Ubuntu/Debian
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49
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50 ```bash
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51 # Install GLPK solver
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52 sudo apt-get update
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53 sudo apt-get install libglpk40 glpk-utils
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54
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55 # Install libvips for SVG processing
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56 sudo apt-get install libvips
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57
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58 # Install Python GLPK bindings
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59 pip install swiglpk
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60 ```
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61
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62 ### macOS
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63
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64 ```bash
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65 # Using Homebrew
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66 brew install glpk vips
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67
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68 # Install Python bindings
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69 pip install swiglpk
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70 ```
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71
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72 ### Windows
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73
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74 ```bash
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75 # Using conda (recommended for Windows)
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76 conda install -c conda-forge glpk
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77
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78 # Or using pip
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79 pip install swiglpk
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80 ```
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81
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82 ## Verify Installation
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83
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84 Test your installation:
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85
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86 ```bash
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87 # Check if COBRAxy tools are available
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88 ras_generator --help
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89 flux_simulation --help
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90
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91 # Test with example data (if available)
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92 cd COBRAxy
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93 python testing.py
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94 ```
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95
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96 ## Troubleshooting Installation
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97
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98 ### Common Issues
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99
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100 **Import Error: No module named 'cobra'**
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101 ```bash
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102 # Install COBRApy manually
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103 pip install cobra
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104 ```
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105
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106 **GLPK solver not found**
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107 ```bash
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108 # Install GLPK solver
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109 # Ubuntu/Debian: sudo apt-get install glpk-utils
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110 # macOS: brew install glpk
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111 # Then: pip install swiglpk
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112 ```
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113
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114 **Permission denied errors**
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115 ```bash
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116 # Use user installation
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117 pip install --user .
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118 # Or use virtual environment (recommended)
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119 python -m venv cobraxy-env
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120 source cobraxy-env/bin/activate # Linux/macOS
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121 # cobraxy-env\Scripts\activate # Windows
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122 pip install .
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123 ```
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124
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125 ## Virtual Environment (Recommended)
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126
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127 Using a virtual environment prevents conflicts with other Python packages:
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128
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129 ```bash
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130 # Create virtual environment
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131 python -m venv cobraxy-env
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132
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133 # Activate environment
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134 source cobraxy-env/bin/activate # Linux/macOS
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135 # cobraxy-env\Scripts\activate # Windows
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136
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137 # Install COBRAxy
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138 pip install .
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139
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140 # When done, deactivate
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141 deactivate
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142 ```
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143
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144 ## Next Steps
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145
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146 After successful installation:
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147
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148 1. **[Quick Start Guide](quickstart.md)** - Run your first analysis
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149 2. **[Tutorial: Python API](tutorials/python-api.md)** - Learn programmatic usage
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150 3. **[Tutorial: Galaxy Setup](tutorials/galaxy-setup.md)** - Set up web interface
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151
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152 ## Getting Help
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153
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154 If you encounter issues:
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155
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156 1. Check the [Troubleshooting Guide](troubleshooting.md)
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157 2. Search [existing issues](https://github.com/CompBtBs/COBRAxy/issues)
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158 3. Create a [new issue](https://github.com/CompBtBs/COBRAxy/issues/new) with:
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159 - Your operating system
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160 - Python version (`python --version`)
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161 - Complete error message
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162 - Installation method used |
