vagrant-provision.py

Just a wrapper around the manual installation process.

Comes with two options:

• vagrant-provision.py –install-system-packages
• vagrant-provision.py –install-pipeline

Install System Packages

Just runs the following in a command shell

python setup.py install_system_packages

Install Pipeline

Essentially runs all the steps after the system package installation for you

• git clone to ~/ngs_mapper
• python setup.py install_python
• setup virtualenv into ~/.ngs_mapper
• activate ~/.ngs_mapper
• python setup.py install