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

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- **[Galaxy Tool Installation](https://planemo.readthedocs.io/en/latest/)**

### COBRAxy-Specific Setup

1. **Copy COBRAxy files** to Galaxy's tools directory:
   ```bash
   mkdir -p tools/cobraxy
   cp /path/to/COBRAxy/*.xml tools/cobraxy/
   cp /path/to/COBRAxy/*.py tools/cobraxy/
   cp -r /path/to/COBRAxy/utils tools/cobraxy/
   cp -r /path/to/COBRAxy/local tools/cobraxy/
   ```

2. **Add tools to Galaxy configuration**:
   Edit `config/tool_conf.xml` and add a COBRAxy section with all tool XML files.

3. **Restart Galaxy** to load the new tools.

**Note**: Consult the official Galaxy documentation for detailed instructions on tool installation, dependency management, and troubleshooting.

- **[Galaxy Workflow Tutorial](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html)**
  - Creating, editing, and sharing workflows
  - Workflow best practices

- **[Workflow Management](https://docs.galaxyproject.org/en/master/user/galaxy_workflow.html)**
  - Official workflow documentation
  - Advanced workflow features

### Example COBRAxy Workflow

A typical COBRAxy workflow might include:

1. **RAS Generator** → Generate activity scores from gene expression

## Additional Resources

### Galaxy Administration Resources

- **[Galaxy Admin Documentation](https://docs.galaxyproject.org/en/master/admin/)**
  - Complete administrator guide
  - Configuration, security, and maintenance

- **[Galaxy Training Materials](https://training.galaxyproject.org/)**
  - Hands-on tutorials for administrators and users
  - Best practices and troubleshooting

- **[Galaxy Community Hub](https://galaxyproject.org/)**
  - Community support and resources
  - Tool repositories and shared workflows

### COBRAxy-Specific Resources

- **Dependencies**: Ensure `cobra`, `pandas`, `numpy`, `scipy` are installed in Galaxy's Python environment
- **Tool Files**: All COBRAxy XML and Python files should be accessible to Galaxy
- **Configuration**: Follow Galaxy's tool installation procedures for proper integration

## Troubleshooting

For troubleshooting Galaxy installations and tool integration issues:

### Official Troubleshooting Resources

- **[Galaxy FAQ](https://docs.galaxyproject.org/en/master/admin/faq.html)**
  - Common installation and configuration issues
  - Performance optimization tips

- **[Galaxy Help Forum](https://help.galaxyproject.org/)**
  - Community-driven support
  - Search existing solutions or ask new questions

- **[Galaxy GitHub Issues](https://github.com/galaxyproject/galaxy/issues)**
  - Report bugs and technical issues
  - Feature requests and discussions

### COBRAxy-Specific Issues

For issues specific to COBRAxy tools in Galaxy:

- **Tool not appearing**: Check tool_conf.xml configuration and restart Galaxy
- **Execution failures**: Verify Python dependencies and file permissions  
- **Parameter errors**: Ensure input data formats match tool requirements

Refer to the [COBRAxy Tools Documentation](../tools/) for detailed parameter information and data format requirements.

## Summary

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.

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- **[Galaxy Tool Installation](https://planemo.readthedocs.io/en/latest/)**

### COBRAxy-Specific Setup

1. **Link COBRAxy to Galaxy tools** directory:
   ```bash
   cd /path/to/galaxy
   ln -s /path/to/COBRAxy/src tools/cobraxy
   ```

2. **Add tools to Galaxy configuration**:
   Edit `config/tool_conf.xml` and add a COBRAxy section:
   ```xml
   <section id="cobraxy" name="COBRAxy">
     <tool file="cobraxy/importMetabolicModel.xml" />
     <tool file="cobraxy/exportMetabolicModel.xml" />
     <tool file="cobraxy/ras_generator.xml" />
     <tool file="cobraxy/rps_generator.xml" />
     <tool file="cobraxy/marea.xml" />
     <tool file="cobraxy/ras_to_bounds.xml" />
     <tool file="cobraxy/flux_simulation.xml" />
     <tool file="cobraxy/flux_to_map.xml" />
     <tool file="cobraxy/marea_cluster.xml" />
   </section>
   ```

3. **Restart Galaxy** to load the new tools.

**Note**: Consult the official Galaxy documentation for detailed instructions on tool installation, dependency management, and troubleshooting.

- **[Galaxy Workflow Tutorial](https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/workflow-editor/tutorial.html)**
  - Creating, editing, and sharing workflows
  - Workflow best practices

### Example COBRAxy Workflow

A typical COBRAxy workflow might include:

1. **RAS Generator** → Generate activity scores from gene expression

## Additional Resources

### Galaxy Administration Resources

- **[Galaxy Training Materials](https://training.galaxyproject.org/)**
  - Hands-on tutorials for administrators and users
  - Best practices and troubleshooting

- **[Galaxy Community Hub](https://galaxyproject.org/)**
  - Community support and resources
  - Tool repositories and shared workflows


## Troubleshooting

For troubleshooting Galaxy installations and tool integration issues:


### COBRAxy-Specific Issues

For issues specific to COBRAxy tools in Galaxy:

- **Tool not appearing**: Check tool_conf.xml configuration and restart Galaxy
- **Execution failures**: Verify Python dependencies and file permissions  
- **Parameter errors**: Ensure input data formats match tool requirements

Refer to the [COBRAxy Tools Documentation](/tools/) for detailed parameter information and data format requirements.

## Summary

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.