Install virtual environment in which to run STEME

    sudo virtualenv --system-site-packages /usr/local/STEME-virtualenv/



Make necessary directories

    sudo mkdir -p /var/lib/STEME
    sudo mkdir -p /var/www/STEME
    sudo mkdir -p /etc/STEME
    sudo chown -R www-data:www-data /var/lib/STEME /var/www/STEME /etc/STEME



Add following to `/etc/apache2/sites-available/default` inside the VirtualHost 

    WSGIDaemonProcess STEME user=www-data group=www-data threads=20
    WSGIScriptAlias /STEME /var/www/STEME/STEME.wsgi
    <Directory /var/www/STEME>
        WSGIProcessGroup STEME
        WSGIApplicationGroup %{GLOBAL}
        Order deny,allow
        Allow from all
    </Directory>
    AliasMatch ^/STEME/result/(.*) /var/lib/STEME/jobs/$1
    <Directory /var/lib/STEME/jobs>
        Order deny,allow
        Allow from all
    </Directory>

and add this before the VirtualHost section

    WSGIPythonHome /usr/local/STEME-virtualenv


Install necessary python libraries

    sudo apt-get install python-psutil
    sudo /usr/local/STEME-virtualenv/bin/pip install flask
    sudo /usr/local/STEME-virtualenv/bin/pip install Flask-SQLAlchemy
    sudo /usr/local/STEME-virtualenv/bin/pip install sqlalchemy
    sudo /usr/local/STEME-virtualenv/bin/pip install Flask-WTF



Download STEME-?.?.?.tar.gz from http://pypi.python.org/pypi/STEME. Unpack and cd into directory. Configure

    sudo /usr/local/STEME-virtualenv/bin/python configure.py --boost-inc-dir= --boost-lib-dir= --seqan-dir=



Build and install

    sudo /usr/local/STEME-virtualenv/bin/python setup.py install



Copy application settings and then edit to configure

    sudo cp python/stemewebapp/default_settings.py /etc/STEME/settings.py
    sudo chown www-data:www-data /etc/STEME/settings.py



Create the database

    sudo -u www-data STEMEWEBAPP_SETTINGS=/etc/STEME/settings.py /usr/local/STEME-virtualenv/bin/stemewebapp-create-db
