comparison COBRAxy/docs/troubleshooting.md @ 547:73f2f7e2be17 draft

Uploaded

546:01147e83f43c

**Problem**: "File not found" errors
```python
# Use absolute paths
from pathlib import Path

tool_dir = str(Path('/path/to/COBRAxy').absolute())
input_file = str(Path('expression.tsv').absolute())

args = ['-td', tool_dir, '-in', input_file, ...]
```

**Problem**: Permission denied
```bash
# Check write permissions

with open('test_input.tsv', 'w') as f:
    f.write(test_data)

# Test basic functionality
ras_generator.main(['-td', tool_dir, '-in', 'test_input.tsv', 
                   '-ra', 'test_output.tsv', '-rs', 'ENGRO2'])
```

### Check Dependencies

### Self-Help Checklist

Before reporting issues:

- ✅ Checked this troubleshooting guide
- ✅ Verified installation completeness
- ✅ Tested with built-in example data
- ✅ Searched existing GitHub issues
- ✅ Tried alternative models/parameters
- ✅ Checked file formats and permissions

## Prevention Tips

### Best Practices

547:73f2f7e2be17

**Problem**: "File not found" errors
```python
# Use absolute paths
from pathlib import Path

input_file = str(Path('expression.tsv').absolute())

args = ['-in', input_file, ...]
```

**Problem**: Permission denied
```bash
# Check write permissions

with open('test_input.tsv', 'w') as f:
    f.write(test_data)

# Test basic functionality
ras_generator.main(['-in', 'test_input.tsv', 
                   '-ra', 'test_output.tsv', '-rs', 'ENGRO2'])
```

### Check Dependencies

### Self-Help Checklist

Before reporting issues:

- Checked this troubleshooting guide
- Verified installation completeness
- Tested with built-in example data
- Searched existing GitHub issues
- Tried alternative models/parameters
- Checked file formats and permissions

## Prevention Tips

### Best Practices