Installing The Source Code

  • If not already installed sudo apt-get install git
  • Navigate to the apprpriate directory (this will be the parent directory of the code)
  • git clone

Installing Python

In order to keep a clean local python environment pyenv needs to be installed:-

  • In your home directory git clone ~/.pyenv
  • echo ‘export PYENV_ROOT=”$HOME/.pyenv”’ >> ~/.bashrc
  • echo ‘export PATH=”$PYENV_ROOT/bin:$PATH”’ >> ~/.bashrc
  • echo ‘eval “$(pyenv init -)”’ >> ~/.bashrc
  • exec $SHELL

Next need to install the correct version of python within pyenv

  • pyenv install 2.7.8

Depending on your system you may have to install the following dependencies:-

  • sudo apt-get install build-essential
  • sudo apt-get install zlib1g-dev
  • sudo apt-get install libssl-dev
  • sudo apt-get install bzip2 libbz2-dev
  • sudo apt-get install libreadline6 libreadline6-dev
  • sudo apt-get install sqlite3 libsqlite3-dev

Installing virtualenv will help manage your virtual environments

  • git clone ~/.pyenv/plugins/pyenv-virtualenv
  • echo ‘eval “$(pyenv virtualenv-init -)”’ >> ~/.bashrc
  • exec “$SHELL”

Now you are ready to create the virtual environment

  • pyenv virtualenv 2.7.8 entero

To activate the environment

  • pyenv activate entero

Next install all the required python packages, which are listed in the requirements.txt file in the base enterobase directory (make sure you are in your virtual environment)

  • pip install -r requirements.txt

Installing an IDE

First install the x2go server such that you open x windows on your local machine

  • sudo add-apt-repository ppa:x2go/stable
  • sudo apt-get update
  • sudo apt-get install x2goserver x2goserver-xsession

Install wing:-

  • tar -xvf wingide-5.1.12-1-x86_64-linux.tar.gz
  • cd wingide-5.1.12-1-x86_64-linux/
  • sudo /home/ubuntu/.pyenv/versions/2.7.8/envs/entero/bin/python
  • echo ‘export PATH=”/usr/local/bin:$PATH”’ >> ~/.bashrc
  • exec “$SHELL”
  • sudo chmod 771 /usr/local/lib/wingide5.1

Wing General Setup

  • In the main menu go to Project>New Project and save it any location (this will just be where the config files are, not the source files). Add the folder where you downloaded the source code once the project is created
  • Make sure you tell wing to use a custom python executable and point it to the python file in your virtual environment (e.g. /home/<user_name>/.pyenev/versions/<virtual_env_name>/bin/Pyhton2.7). N.B Right click on the file popup in order to see hidden files and navigate to to .pyenv directory.

Debugging with Wing:-

  • Copy the and wingdb-suid from /usr/local/lib/wingide5.1 (or wherever you installed wing) to the main app directory i.e.entero
  • Make sure that import wingdbstub is in the enterobase code, usually located in create_app method of the main entero __init__ method
  • When wing is open, right click on the bug in the bottom left and make sure Accept Debug Connections is checked
  • Then run the website in the normal way
  • In the gunicorn start up script, make sure you set the —timeout parameter to 2000 (or greater), else you will only get 30 seconds to debug

Running the app with Gunicorn

create a file called with the following content

FLASKDIR=/var/www/enterobase   # Change this to location of
SOCKFILE=/var/www/enterobase/sock # change this to project_dir/sock (new file will be created)
USER=ubuntu                        # Change this to your user/group
echo "Starting $NAME as `whoami`"


# Create the run directory if it doesn't exist
test -d $RUNDIR || mkdir -p $RUNDIR


# Start your unicorn
exec /home/$USER/.pyenv/versions/enterobase/bin/gunicorn "ssbase:create_app()" -b \
  --enable-stdio-inheritance \
  --access-logfile=$LOG/access.log \
  --error-logfile=$LOG/error.log \
  --log-level=debug \
  --name $NAME \
  --workers $NUM_WORKERS \
  --user=$USER --group=$GROUP \
  --log-file=$LOG/gunilog.log \
  --bind=unix:$SOCKFILE \
  --timeout 2000

The app can be run with nohup & , but using supervisor may be more appropriate

Installing the Nginx Server

Install nginx sudo apt-get install nginx in /etc/nginx/sites_enabled

server {
        listen 80;
        server_name ip_address;
        location / {
                proxy_pass http://localhost:8000;

In order to update nginx with the changes:- sudo nginx -s reload

Allowing Emails

On Jenner you need to add the IP address of the new server:-

  • sudo vim /etc/postfix/
  • Add the IP address in parameter “mynetworks = “
  • sudo /etc/init.d/postfix restart