OMERO.web installation separately from OMERO.server on CentOS 7 and IcePy 3.6

Please first read OMERO.server installation on CentOS 7.

This is an example walkthrough for installing OMERO.web decoupled from the OMERO.server in a virtual environment using OMERO.py and a dedicated system user. Installing OMERO.web in a virtual environment is the preferred way. For convenience in this walkthrough, we will use the omero system user and define the main OMERO.web configuration options as environment variables.

The following steps are run as root.

If required, first create a local system user omero and create the homedir too /home/omero:

useradd -m omero

chmod a+X /home/omero

Installing prerequisites

The following steps are run as root.

Install ZeroC IcePy 3.6. IcePy is managed by PyPI, a package management system used to install and manage software packages written in Python. IcePy will be installed as part of the OMERO.web requirements:

yum -y install gcc gcc-c++ python-devel

yum -y install libdb-utils openssl-devel bzip2-devel

# reset the locale changed by installing gcc
localedef -i en_US -f UTF-8 en_US.UTF-8

Install other dependencies. The number of dependencies to install depends on the way you plan to install OMERO.web. If you wish to install it in a virtual environment created with --system-site-packages on (option 1), you will need to install python-pillow and numpy. If you wish to install it in a virtual environment with --system-site-packages off, a few more dependencies will be required (option 2):

# dependencies common to both options
yum -y install epel-release

yum -y install unzip

yum -y install python-pip

yum -y install nginx

# install the latest version
pip install --upgrade pip
pip install --upgrade virtualenv

# To install OMERO.web using option 1
yum -y install python-pillow numpy

# To install OMERO.web using option 2
yum -y install python-devel libjpeg-devel libtiff libtiff-devel zlib-devel

Creating a virtual environment

The following steps are run as the omero system user.

Create the virtual environment. This is the preferred way to install OMERO.web:

# option 1: in a virtual environment with --system-site-packages on
virtualenv /home/omero/omerowebvenv --system-site-packages

# option 2: in a virtual environment with --system-site-packages off
virtualenv /home/omero/omerowebvenv

Installing OMERO.web

The following steps are run as the omero system user.

Install OMERO.web using OMERO.py:

cd /home/omero
curl -o OMERO.py.zip -L https://downloads.openmicroscopy.org/latest/omero5/py.zip
unzip -q OMERO.py*

zip=$(ls OMERO.py*.zip)
rm -f $zip
ln -s OMERO.py-* OMERO.py

The following steps are run as the omero system user.

Install the OMERO.web requirements. Select one of the commands corresponding to the way you have opted to install it:

# option 1: in a virtual environment with --system-site-packages on
/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27.txt

# option 2: in a virtual environment with --system-site-packages off
/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27-all.txt

Installing OMERO.web apps

The following steps are run as the omero system user.

A number of apps are available to add functionality to OMERO.web, such as OMERO.figure and OMERO.iviewer. See the main website for a list of released apps. These apps are optional and can be installed via pip to your OMERO.web virtual environment at any time.

Configuring OMERO.web

The following steps are run as the omero system user.

For convenience the main OMERO.web configuration options have been defined as environment variables. You can either use your own values, or alternatively use the following ones:

export WEBPORT=80
export WEBSERVER_NAME=localhost

Configure OMERO.web and create the NGINX OMERO configuration file:

. /home/omero/omerowebvenv/bin/activate

/home/omero/OMERO.py/bin/omero config set omero.web.application_server wsgi-tcp
/home/omero/OMERO.py/bin/omero web config nginx --http "${WEBPORT}" --servername "${WEBSERVER_NAME}" > /home/omero/nginx.conf.tmp

For more customization, please read Customizing your OMERO.web installation.

Configuring Gunicorn

The following steps are run as the omero system user.

Additional settings can be configured by changing the following properties:

Configuring NGINX

The following steps are run as root.

Copy the generated configuration file into the NGINX configuration directory, disable the default configuration and start NGINX:

sed -i.bak -re 's/( default_server.*)/; #\1/' /etc/nginx/nginx.conf
if [ -f /etc/nginx/conf.d/default.conf ]; then
    mv /etc/nginx/conf.d/default.conf /etc/nginx/conf.d/default.disabled
fi
cp /home/omero/nginx.conf.tmp /etc/nginx/conf.d/omeroweb.conf

systemctl enable nginx

systemctl start nginx

Running OMERO.web

The following steps are run as the omero system user.

Install WhiteNoise:

. /home/omero/omerowebvenv/bin/activate

pip install --upgrade 'whitenoise<4'

Configure WhiteNoise and start OMERO.web manually to test the installation:

. /home/omero/omerowebvenv/bin/activate

/home/omero/OMERO.py/bin/omero config append -- omero.web.middleware '{"index": 0, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}'

/home/omero/OMERO.py/bin/omero web start

# Test installation e.g. curl -sL localhost:4080

/home/omero/OMERO.py/bin/omero web stop

Automatically running OMERO.web

The following steps are run as root.

Should you wish to run OMERO.web automatically, a systemd.service file could be created. See below an example file omero-web-systemd.service:

[Unit]
Description=OMERO.web
# Not mandatory, NGINX may be running on a different server
Requires=nginx.service
After=network.service

[Service]
User=omero
Type=forking
PIDFile=/home/omero/OMERO.py/var/django.pid
Restart=no
RestartSec=10
Environment="PATH=/home/omero/omerowebvenv/bin:/bin:/usr/bin"
ExecStart=/home/omero/omerowebvenv/bin/python /home/omero/OMERO.py/bin/omero web start
ExecStop=/home/omero/omerowebvenv/bin/python /home/omero/OMERO.py/bin/omero web stop

[Install]
WantedBy=multi-user.target

Copy the systemd.service file, then enable and start the service:

cp omero-web-systemd.service /etc/systemd/system/omero-web.service

systemctl daemon-reload

systemctl enable omero-web.service

systemctl stop omero-web.service

systemctl start omero-web.service

Maintenance

The following steps are run as the omero system user.

Please read OMERO.web maintenance.

SELinux

The following steps are run as root.

If you are running a system with SELinux enabled and are unable to access OMERO.web you may need to adjust the security policy:

if [ $(getenforce) != Disabled ]; then

    yum -y install policycoreutils-python
    setsebool -P httpd_read_user_content 1
    setsebool -P httpd_enable_homedirs 1
    semanage port -a -t http_port_t -p tcp 4080

fi