Note

This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.

OMERO.web walkthrough installation CentOS 7 and IcePy 3.6

For convenience in this walkthrough the main OMERO.web configuration options have been defined as environment variables. When following this walkthrough you can either use your own values, or alternatively source the following file:

OMERO_USER=omero
WEBPORT=80
WEBSERVER_NAME=localhost

Create local user omero, homedir /home/omero (run as root):

if [ -z "$(getent passwd omero)" ]; then

    useradd -m omero

fi

chmod a+X /home/omero

Install ZeroC IcePy 3.6. IcePy is managed by PyPI and will be installed as a part of OMERO.web requirements (run as root):

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

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

Install other dependencies (run as root):

yum -y install epel-release

yum -y install python-pip

yum -y install \
    python-pillow \
    numpy


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

Install VirtualEnv - optional (run as root):

virtualenv /home/omero/omerowebvenv --system-site-packages

Install OMERO.web (run as omero):

curl -o OMERO.py.zip https://downloads.openmicroscopy.org/latest/omero5.3/py.zip

zip=$(ls OMERO.py*.zip)
zipname=${zip%.zip}
rm -f $zip
mv $(find . -name 'OMERO.py*' -type d) /home/omero/OMERO.py

Install VirtualEnv (run as root):

/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27.txt

Configure OMERO.web and generate nginx template (run as omero):

source /home/omero/omerowebvenv/bin/activate

if [[ $WEBPREFIX = *[!\ ]* ]]; then
    /home/omero/OMERO.py/bin/omero config set omero.web.prefix "${WEBPREFIX}"
    /home/omero/OMERO.py/bin/omero config set omero.web.static_url "${WEBPREFIX}/static/"
fi

/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

cat /home/omero/nginx.conf.tmp

Install NGINX (run as root):

yum -y install 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

Disable SELINUX (run as root):

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

Daemon (run as root):

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

systemctl daemon-reload

systemctl enable omero-web.service

systemctl start omero-web.service

omero-web-systemd.service example:

[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/venv/bin:/bin:/usr/bin" "WEBBINDIR=/home/omero/OMERO.py/bin"
ExecStart=/home/omero/omerowebvenv/venv/python $WEBBINDIR/omero web start
ExecStop=/home/omero/omerowebvenv/venv/python $WEBBINDIR/omero web stop

[Install]
WantedBy=multi-user.target