UPGRADE.md

If you activate the pipeline via ngs_mapper/setup

• Completely remove the existing ngs_mapper directory.
• Then follow INSTALL.md

If you installed using setup.py

1. First fetch any possible updates

```cd ~/ngs_mapper; git fetch```

2. Then check if you need to update

```
git status | grep -q 'Your branch is behind' && echo 'You need to update' || echo 'You are up-to-date'
```

- If it returns You are up-to-date you are done

3. Update(pull new code)

```
git pull
```

4. Reinstall

Then follow [INSTALL.md](INSTALL.md) starting with section #2