upgrade.rst

Upgrade

If you activate the pipeline via ngs_mapper/setup

• Completely remove the existing ngs_mapper directory.
• Then follow install

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. Go into your ngs_mapper directory and rerun the setup script

   python setup.py install