--- a/COBRAxy/docs/getting-started.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/getting-started.md	Sun Oct 26 19:27:41 2025 +0000
@@ -74,7 +74,8 @@
 
 ```bash
 # Generate RAS from expression data
-ras_generator -td $(pwd) \
+# Note: -td is optional and auto-detected after pip install
+ras_generator \
   -in expression_data.tsv \
   -ra ras_output.tsv \
   -rs ENGRO2
@@ -84,7 +85,8 @@
 
 ```bash
 # Generate enriched pathway maps
-marea -td $(pwd) \
+# Note: -td is optional and auto-detected after pip install
+marea \
   -using_RAS true \
   -input_data ras_output.tsv \
   -choice_map ENGRO2 \
@@ -108,7 +110,7 @@
 | **ENGRO2** | Human | ~2,000 | ~500 | Focused human metabolism model |
 | **Recon** | Human | ~10,000 | ~2,000 | Comprehensive human metabolism |
 
-Models are stored in the `local/` directory and include:
+Models are stored in the `src/local/` directory and include:
 - SBML files
 - GPR rules  
 - Gene mapping tables
@@ -132,34 +134,17 @@
 lactate	23.9	41.2	19.4
 ```
 
-## Command Line vs Python API
-
-COBRAxy offers two usage modes:
-
-### Command Line (Quick Analysis)
-```bash
-# Simple command-line execution
-ras_generator -td $(pwd) -in data.tsv -ra output.tsv -rs ENGRO2
-```
-
-### Python API (Programming)
-```python
-import ras_generator
-# Call main function with arguments
-ras_generator.main(['-td', '/path', '-in', 'data.tsv', '-ra', 'output.tsv', '-rs', 'ENGRO2'])
-```
-
 ## Next Steps
 
 Now that you understand the basics:
 
-1. **[Quick Start Guide](quickstart.md)** - Complete walkthrough with example data
-2. **[Python API Tutorial](tutorials/python-api.md)** - Learn programmatic usage
-3. **[Tools Reference](tools/)** - Detailed documentation for each tool
-4. **[Examples](examples/)** - Real-world analysis examples
+1. **[Quick Start Guide](/quickstart.md)** - Complete walkthrough with example data
+2. **[Galaxy Tutorial](/tutorials/galaxy-setup.md)** - Web-based analysis setup
+3. **[Tools Reference](/tools/)** - Detailed documentation for each tool
+4. **[Examples](/examples/)** - Real-world analysis examples
 
 ## Need Help?
 
-- **[Troubleshooting](troubleshooting.md)** - Common issues and solutions
+- **[Troubleshooting](/troubleshooting.md)** - Common issues and solutions
 - **[GitHub Issues](https://github.com/CompBtBs/COBRAxy/issues)** - Report bugs or ask questions
-- **[Contributing](contributing.md)** - Help improve COBRAxy
\ No newline at end of file
+- **[Contributing](/contributing.md)** - Help improve COBRAxy
\ No newline at end of file