Mercurial > repos > bimib > cobraxy

comparison COBRAxy/docs/installation.md @ 538:fd53d42348bd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Sat, 25 Oct 2025 11:39:03 +0000
parents 4ed95023af20
children fcdbc81feb45
comparison
equal deleted inserted replaced
537:f79250e824b5 538:fd53d42348bd
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**: 3.8-3.11 7 - **Python**: 3.8-3.12
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 - **Storage**: 2GB free space for installation and temporary files
10 10
11 ## Quick Install 11 ## Quick Install
12 12
32 pip install -e . 32 pip install -e .
33 ``` 33 ```
34 34
35 ## Dependencies 35 ## Dependencies
36 36
37 COBRAxy automatically installs its Python dependencies: 37 COBRAxy automatically installs its Python dependencies (COBRApy, pandas, numpy, etc.)
38
39 - **COBRApy** - Core metabolic modeling
40 - **pandas** - Data manipulation
41 - **numpy** - Numerical computations
42 - **scipy** - Scientific computing
43
44 ## Optional System Libraries
45
46 Install additional libraries for enhanced features:
47
48 ### Ubuntu/Debian
49
50 ```bash
51 # Install GLPK solver
52 sudo apt-get update
53 sudo apt-get install libglpk40 glpk-utils
54
55 # Install libvips for SVG processing
56 sudo apt-get install libvips
57
58 # Install Python GLPK bindings
59 pip install swiglpk
60 ```
61
62 ### macOS
63
64 ```bash
65 # Using Homebrew
66 brew install glpk vips
67
68 # Install Python bindings
69 pip install swiglpk
70 ```
71
72 ### Windows
73
74 ```bash
75 # Using conda (recommended for Windows)
76 conda install -c conda-forge glpk
77
78 # Or using pip
79 pip install swiglpk
80 ```
81 38
82 ## Verify Installation 39 ## Verify Installation
83 40
84 Test your installation: 41 Test your installation:
85 42
86 ```bash 43 ```bash
87 # Check if COBRAxy tools are available 44 # Check if COBRAxy tools are available
88 ras_generator --help 45 ras_generator --help
89 flux_simulation --help 46 flux_simulation --help
90
91 # Test with example data (if available)
92 cd COBRAxy
93 python testing.py
94 ```
95
96 ## Troubleshooting Installation
97
98 ### Common Issues
99
100 **Import Error: No module named 'cobra'**
101 ```bash
102 # Install COBRApy manually
103 pip install cobra
104 ```
105
106 **GLPK solver not found**
107 ```bash
108 # Install GLPK solver
109 # Ubuntu/Debian: sudo apt-get install glpk-utils
110 # macOS: brew install glpk
111 # Then: pip install swiglpk
112 ```
113
114 **Permission denied errors**
115 ```bash
116 # Use user installation
117 pip install --user .
118 # Or use virtual environment (recommended)
119 python -m venv cobraxy-env
120 source cobraxy-env/bin/activate # Linux/macOS
121 # cobraxy-env\Scripts\activate # Windows
122 pip install .
123 ``` 47 ```
124 48
125 ## Virtual Environment (Recommended) 49 ## Virtual Environment (Recommended)
126 50
127 Using a virtual environment prevents conflicts with other Python packages: 51 Using a virtual environment prevents conflicts with other Python packages: