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UPGRADE.md

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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```
  1. 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
  1. Update(pull new code)
```
git pull
```
  1. Reinstall
Then follow [INSTALL.md](INSTALL.md) starting with section #2