Deploy D‐Genies in webserver mode with apache

For this recipe, we will use CentOS 7 as Linux distribution.

Note: All this recipe commands will be done as root user, or prefixed with sudo.

Install D-Genies

Requirements

We will install D-Genies as root user, but D-Genies will be run by the user dgenies. We create then the user dgenies:

# We add the user
useradd -m dgenies

# We can also set the user password
passwd dgenies

By default, CentOS is installed with SELinux activated and in Enforcing state. We disable it in order to avoid interference with D-Genies installation and configuration.

# We deactivate SELinux (need to reboot to be taken in account)
sed -i 's/^SELINUX=.*/SELINUX=disabled/' /etc/selinux/config 
# Set SELinux in permissive state now! This way, we don't need to reboot.
setenforce 0

We also deactivate the firewall for the same reason

systemctl stop firewalld
systemctl disable firewalld

D-Genies is written for Python 3.5+, which can be installed with the following command:

yum install -y python3 python3-devel python3-pip

D-Genies also needs the following system dependencies.

yum install -y  "@Development tools" time zlib-devel libjpeg-turbo-devel libsq3-devel sqlite-devel

Install D-Genies

We can install D-Genies from source.

cd /tmp
git clone https://github.com/genotoul-bioinfo/dgenies.git dgenies.git
cd gdenies.git
python3 setup.py install

We can also use pip, but pip behaviour has changed over time. Recent pip versions do not copy some D-Genies files in the right place anymore. If you want to try, you can use the following command:

python3 -m pip install dgenies

Configure D-Genies

From this step, you can configure D-Genies by editing the /etc/dgenies/application.properties file and run it directly with the dgenies run -m webserver command, but it is not the way to serve wsgi application in production mode.

We also recommend to use a MySQL/MariaDB database instead of the SQLite one use by default by D-Genies

TO DEVELOP

Use apache to serve flask application

Install apache2 with mod_wsgi

yum install -y httpd epel-release
yum install -y python3-mod_wsgi

Configuration

We create the /etc/httpd/conf.d/dgenies.conf file with following content:

<VirtualHost *>
    ServerName <url>

    WSGIDaemonProcess dgenies user=dgenies group=dgenies threads=8
    WSGIScriptAlias / /var/www/dgenies/dgenies.wsgi

    <Directory /var/www/dgenies>
        WSGIProcessGroup dgenies
        WSGIApplicationGroup %{GLOBAL}
        Order deny,allow
        Allow from all
    </Directory>
</VirtualHost>

where <url> is your server address

Running D-Genies

Now we can start D-Genies:

systemctl start httpd
systemctl enable httpd

D-Genies can be stopped this way:

# We stop the flask application
systemctl stop httpd

# We can also stop the local scheduler launched by the flask app.
sudo -u dgenies dgenies clear -c