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comparison COBRAxy/docs/tutorials/galaxy-setup.md @ 542:fcdbc81feb45 draft

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
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42 42
43 - **[Galaxy Tool Installation](https://planemo.readthedocs.io/en/latest/)** 43 - **[Galaxy Tool Installation](https://planemo.readthedocs.io/en/latest/)**
44 44
45 ### COBRAxy-Specific Setup 45 ### COBRAxy-Specific Setup
46 46
47 1. **Copy COBRAxy files** to Galaxy's tools directory: 47 1. **Link COBRAxy to Galaxy tools** directory:
48 ```bash 48 ```bash
49 mkdir -p tools/cobraxy 49 cd /path/to/galaxy
50 cp /path/to/COBRAxy/*.xml tools/cobraxy/ 50 ln -s /path/to/COBRAxy/src tools/cobraxy
51 cp /path/to/COBRAxy/*.py tools/cobraxy/
52 cp -r /path/to/COBRAxy/utils tools/cobraxy/
53 cp -r /path/to/COBRAxy/local tools/cobraxy/
54 ``` 51 ```
55 52
56 2. **Add tools to Galaxy configuration**: 53 2. **Add tools to Galaxy configuration**:
57 Edit `config/tool_conf.xml` and add a COBRAxy section with all tool XML files. 54 Edit `config/tool_conf.xml` and add a COBRAxy section:
55 ```xml
56 <section id="cobraxy" name="COBRAxy">
57 <tool file="cobraxy/importMetabolicModel.xml" />
58 <tool file="cobraxy/exportMetabolicModel.xml" />
59 <tool file="cobraxy/ras_generator.xml" />
60 <tool file="cobraxy/rps_generator.xml" />
61 <tool file="cobraxy/marea.xml" />
62 <tool file="cobraxy/ras_to_bounds.xml" />
63 <tool file="cobraxy/flux_simulation.xml" />
64 <tool file="cobraxy/flux_to_map.xml" />
65 <tool file="cobraxy/marea_cluster.xml" />
66 </section>
67 ```
58 68
59 3. **Restart Galaxy** to load the new tools. 69 3. **Restart Galaxy** to load the new tools.
60 70
61 **Note**: Consult the official Galaxy documentation for detailed instructions on tool installation, dependency management, and troubleshooting. 71 **Note**: Consult the official Galaxy documentation for detailed instructions on tool installation, dependency management, and troubleshooting.
62 72
86 96
87 - **[Galaxy Workflow Tutorial](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html)** 97 - **[Galaxy Workflow Tutorial](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html)**
88 - Creating, editing, and sharing workflows 98 - Creating, editing, and sharing workflows
89 - Workflow best practices 99 - Workflow best practices
90 100
91 - **[Workflow Management](https://docs.galaxyproject.org/en/master/user/galaxy_workflow.html)**
92 - Official workflow documentation
93 - Advanced workflow features
94
95 ### Example COBRAxy Workflow 101 ### Example COBRAxy Workflow
96 102
97 A typical COBRAxy workflow might include: 103 A typical COBRAxy workflow might include:
98 104
99 1. **RAS Generator** → Generate activity scores from gene expression 105 1. **RAS Generator** → Generate activity scores from gene expression
104 110
105 ## Additional Resources 111 ## Additional Resources
106 112
107 ### Galaxy Administration Resources 113 ### Galaxy Administration Resources
108 114
109 - **[Galaxy Admin Documentation](https://docs.galaxyproject.org/en/master/admin/)**
110 - Complete administrator guide
111 - Configuration, security, and maintenance
112
113 - **[Galaxy Training Materials](https://training.galaxyproject.org/)** 115 - **[Galaxy Training Materials](https://training.galaxyproject.org/)**
114 - Hands-on tutorials for administrators and users 116 - Hands-on tutorials for administrators and users
115 - Best practices and troubleshooting 117 - Best practices and troubleshooting
116 118
117 - **[Galaxy Community Hub](https://galaxyproject.org/)** 119 - **[Galaxy Community Hub](https://galaxyproject.org/)**
118 - Community support and resources 120 - Community support and resources
119 - Tool repositories and shared workflows 121 - Tool repositories and shared workflows
120 122
121 ### COBRAxy-Specific Resources
122
123 - **Dependencies**: Ensure `cobra`, `pandas`, `numpy`, `scipy` are installed in Galaxy's Python environment
124 - **Tool Files**: All COBRAxy XML and Python files should be accessible to Galaxy
125 - **Configuration**: Follow Galaxy's tool installation procedures for proper integration
126 123
127 ## Troubleshooting 124 ## Troubleshooting
128 125
129 For troubleshooting Galaxy installations and tool integration issues: 126 For troubleshooting Galaxy installations and tool integration issues:
130 127
131 ### Official Troubleshooting Resources
132
133 - **[Galaxy FAQ](https://docs.galaxyproject.org/en/master/admin/faq.html)**
134 - Common installation and configuration issues
135 - Performance optimization tips
136
137 - **[Galaxy Help Forum](https://help.galaxyproject.org/)**
138 - Community-driven support
139 - Search existing solutions or ask new questions
140
141 - **[Galaxy GitHub Issues](https://github.com/galaxyproject/galaxy/issues)**
142 - Report bugs and technical issues
143 - Feature requests and discussions
144 128
145 ### COBRAxy-Specific Issues 129 ### COBRAxy-Specific Issues
146 130
147 For issues specific to COBRAxy tools in Galaxy: 131 For issues specific to COBRAxy tools in Galaxy:
148 132
149 - **Tool not appearing**: Check tool_conf.xml configuration and restart Galaxy 133 - **Tool not appearing**: Check tool_conf.xml configuration and restart Galaxy
150 - **Execution failures**: Verify Python dependencies and file permissions 134 - **Execution failures**: Verify Python dependencies and file permissions
151 - **Parameter errors**: Ensure input data formats match tool requirements 135 - **Parameter errors**: Ensure input data formats match tool requirements
152 136
153 Refer to the [COBRAxy Tools Documentation](../tools/) for detailed parameter information and data format requirements. 137 Refer to the [COBRAxy Tools Documentation](/tools/) for detailed parameter information and data format requirements.
154 138
155 ## Summary 139 ## Summary
156 140
157 This tutorial provides guidance for setting up Galaxy with COBRAxy tools by referencing official Galaxy documentation. For detailed installation procedures, always consult the official Galaxy administrator guides, as they are regularly updated with the latest best practices and troubleshooting information. 141 This tutorial provides guidance for setting up Galaxy with COBRAxy tools by referencing official Galaxy documentation. For detailed installation procedures, always consult the official Galaxy administrator guides, as they are regularly updated with the latest best practices and troubleshooting information.
158 142