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

Uploaded

--- a/COBRAxy/docs/tutorials/galaxy-setup.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/tutorials/galaxy-setup.md	Sun Oct 26 19:27:41 2025 +0000
@@ -44,17 +44,27 @@
 
 ### COBRAxy-Specific Setup
 
-1. **Copy COBRAxy files** to Galaxy's tools directory:
+1. **Link COBRAxy to Galaxy 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/
+   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 with all tool XML files.
+   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.
 
@@ -88,10 +98,6 @@
   - 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:
@@ -106,10 +112,6 @@
 
 ### 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
@@ -118,29 +120,11 @@
   - 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
 
@@ -150,7 +134,7 @@
 - **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.
+Refer to the [COBRAxy Tools Documentation](/tools/) for detailed parameter information and data format requirements.
 
 ## Summary