OMERO.web installation 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 in a virtual environment using 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-web system user and define the main OMERO.web configuration options as environment variables. Since 5.6, a new OMERODIR
variable is used, you should first unset OMERO_HOME
(if set) before beginning the installation process.
The following steps are run as root.
If required, first create a local system user omero-web and create directory:
useradd -m omero-web
mkdir -p /opt/omero/web/omero-web/etc/grid
chown -R omero-web /opt/omero/web/omero-web
Installing prerequisites¶
The following steps are run as root.
Install dependencies:
yum -y install epel-release
yum -y install unzip
yum -y install python3
yum -y install nginx
Optional: if you wish to use the Redis cache, install Redis:
yum -y install redis python-redis
systemctl enable redis.service
systemctl start redis.service
Creating a virtual environment¶
The following steps are run as root.
Create the virtual environment. This is the recommended way to install OMERO.web:
python3 -mvenv /opt/omero/web/venv3
Install ZeroC IcePy 3.6:
/opt/omero/web/venv3/bin/pip install --upgrade https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl
Install OMERO.web:
/opt/omero/web/venv3/bin/pip install "omero-web>=5.6.3"
Installing OMERO.web apps¶
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, as the root user, via pip to your OMERO.web virtual environment and configured as the omero-web system user, at any time.
Configuring OMERO.web¶
The following steps are run as the omero-web 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 WEBSESSION=True
export OMERODIR=/opt/omero/web/omero-web
export WEBPORT=80
export WEBSERVER_NAME=localhost
Configure OMERO.web and create the NGINX OMERO configuration file:
export PATH=/opt/omero/web/venv3/bin:$PATH
omero config set omero.web.application_server wsgi-tcp
omero web config nginx --http "${WEBPORT}" --servername "${WEBSERVER_NAME}" > /opt/omero/web/omero-web/nginx.conf.tmp
For more customization, please read Customizing your OMERO.web installation.
Configuring Gunicorn¶
The following steps are run as the omero-web system user.
Additional settings can be configured by changing the properties below. Before changing the properties, run
export PATH=/opt/omero/web/venv3/bin:$PATH
:
omero.web.wsgi_workers
to (2 x NUM_CORES) + 1Note
Do not scale the number of workers to the number of clients you expect to have. OMERO.web should only need 4-12 worker processes to handle many requests per second.
omero.web.wsgi_args
Additional arguments. For more details check Gunicorn Documentation.
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 /opt/omero/web/omero-web/nginx.conf.tmp /etc/nginx/conf.d/omeroweb.conf
systemctl enable nginx
systemctl start nginx
Running OMERO.web¶
The following steps are run as root.
Install WhiteNoise:
/opt/omero/web/venv3/bin/pip install --upgrade 'whitenoise<4'
Optional: Install Django Redis:
/opt/omero/web/venv3/bin/pip install 'django-redis<4.9'
The following steps are run as the omero-web system user.
Optional: Configure the cache:
omero config set omero.web.caches '{"default": {"BACKEND": "django_redis.cache.RedisCache","LOCATION": "redis://127.0.0.1:6379/0"}}'
omero config set omero.web.session_engine 'django.contrib.sessions.backends.cache'
Configure WhiteNoise and start OMERO.web manually to test the installation:
omero config append -- omero.web.middleware '{"index": 0, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}'
omero web start
# Test installation e.g. curl -sL localhost:4080
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-web
Type=forking
PIDFile=/opt/omero/web/omero-web/var/django.pid
Restart=no
RestartSec=10
Environment="PATH=/opt/omero/web/venv3/bin:/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin""
Environment="OMERODIR=/opt/omero/web/omero-web"
ExecStart=/opt/omero/web/venv3/bin/omero web start
ExecStop=/opt/omero/web/venv3/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-web 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