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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 ## System Dependencies
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12
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13 Install required build tools before installing COBRAxy:
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14
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15 ```bash
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16 # Ubuntu/Debian
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17 sudo apt-get install build-essential cmake pkg-config libvips libglpk40 glpk-utils
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18
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19 # macOS
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20 xcode-select --install
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21 brew install cmake pkg-config vips glpk
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22
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23 # Windows (with Chocolatey)
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24 choco install cmake visualstudio2022buildtools pkgconfiglite
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25 ```
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26
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27 ## Installation Methods
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28
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29 ### Recommended: Using Conda
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30
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31 Create an isolated environment with all dependencies:
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32
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33 ```bash
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34 # Create a new conda environment
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35 conda create -n cobraxy python=3.13 -y
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36 conda activate cobraxy
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37
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38 # Install build tools via conda
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39 conda install -c conda-forge cmake pkg-config swiglpk -y
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40
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41 # Clone and install COBRAxy
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42 git clone https://github.com/CompBtBs/COBRAxy.git
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43 cd COBRAxy/src
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44 pip install .
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45 ```
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46
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47 ### Alternative: Direct Installation
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48
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49 If you have system dependencies already installed:
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50
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51 ```bash
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52 # Clone the repository
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53 git clone https://github.com/CompBtBs/COBRAxy.git
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54 cd COBRAxy/src
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55
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56 # Install COBRAxy
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57 pip install .
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58 ```
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59
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60 ### Development Install
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61
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62 For development or if you want to modify COBRAxy:
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63
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64 ```bash
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65 # Clone and install in editable mode
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66 git clone https://github.com/CompBtBs/COBRAxy.git
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67 cd COBRAxy/src
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68 pip install -e .
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69 ```
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70
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71 ## Verify Installation
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72
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73 Test your installation:
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74
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75 ```bash
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76 # Check if COBRAxy tools are available
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77 ras_generator --help
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78 flux_simulation --help
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79 marea --help
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80
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81 # Check Python can import COBRAxy modules
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82 python -c "import ras_generator; print('COBRAxy installed successfully!')"
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83 ```
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84
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85 ## Troubleshooting Installation
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86
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87 ### Missing Compiler Errors
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88
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89 If you see errors about missing compilers during installation:
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90
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91 ```bash
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92 # Ubuntu/Debian
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93 sudo apt-get install build-essential
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94
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95 # macOS
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96 xcode-select --install
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97 ```
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98
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99 ### CMake Not Found
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100
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101 ```bash
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102 # Ubuntu/Debian
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103 sudo apt-get install cmake
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104
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105 # macOS
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106 brew install cmake
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107
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108 # Or via conda
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109 conda install -c conda-forge cmake
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110 ```
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111
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112 ### pkg-config Issues
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113
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114 ```bash
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115 # Ubuntu/Debian
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116 sudo apt-get install pkg-config
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117
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118 # macOS
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119 brew install pkg-config
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120
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121 # Or via conda
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122 conda install -c conda-forge pkg-config
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123 ```
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124
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125 ## Alternative: Virtual Environment (without Conda)
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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 cd COBRAxy/src
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139 pip install .
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140
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141 # When done, deactivate
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142 deactivate
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143 ```
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144
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145 ## Next Steps
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146
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147 After successful installation:
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148
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149 1. **[Quick Start Guide](/quickstart.md)** - Run your first analysis
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150 2. **[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 |
