Note
This documentation is for the new OMERO 5.2 version. See the latest OMERO 5.1.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.
This is an example walkthrough for installing OMERO on Ubuntu, using a dedicated system user, and should be read in conjunction with OMERO.web deployment. You can use this as a guide for setting up your own test server. For production use you should also read the pages listed under Optimizing Server Configuration.
Example shell scripts for installing OMERO on Ubuntu 14.04 are included in-line, and can be downloaded. These instructions assume your Linux distribution is configured with a UTF-8 locale (this is normally the default).
For convenience in this walkthrough the main OMERO 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_DB_USER=db_user
OMERO_DB_PASS=db_password
OMERO_DB_NAME=omero_database
OMERO_ROOT_PASS=omero_root_password
OMERO_DATA_DIR=/OMERO
OMERO_WEB_PORT=80
export OMERO_DB_USER OMERO_DB_PASS OMERO_DB_NAME OMERO_ROOT_PASS OMERO_DATA_DIR OMERO_WEB_PORT
export PGPASSWORD="$OMERO_DB_PASS"
The following steps are run as root.
Install Ice, Java, PostgreSQL:
#!/bin/bash
apt-get update
apt-get -y install \
unzip \
wget \
python-{matplotlib,numpy,pip,scipy,tables,virtualenv} \
openjdk-7-jre-headless \
ice-services python-zeroc-ice \
postgresql
# require to install Pillow
apt-get -y install \
libtiff5-dev \
libjpeg8-dev \
zlib1g-dev \
libfreetype6-dev \
liblcms2-dev \
libwebp-dev \
tcl8.6-dev \
tk8.6-dev
pip install --upgrade "Pillow<3.0"
# Django
pip install "Django>=1.8,<1.9"
service postgresql start
Create an omero system user, and a directory for the OMERO repository:
#!/bin/bash
useradd -m omero
chmod a+X ~omero
mkdir -p "$OMERO_DATA_DIR"
chown omero "$OMERO_DATA_DIR"
Create a database user and initialize a new database for OMERO:
#!/bin/bash
source settings.env
echo "CREATE USER $OMERO_DB_USER PASSWORD '$OMERO_DB_PASS'" | \
su - postgres -c psql
su - postgres -c "createdb -E UTF8 -O '$OMERO_DB_USER' '$OMERO_DB_NAME'"
psql -P pager=off -h localhost -U "$OMERO_DB_USER" -l
The following steps are run as the omero system user.
Download, unzip and configure OMERO, and create a configuration file for Nginx. The rest of this walkthrough assumes the OMERO.server is installed into the home directory of the omero system user.
Note that this script requires the same environment variables that were set earlier in settings.env, so you may need to copy and/or source this file as the omero user.
#!/bin/bash
set -e -u -x
source settings.env
SERVER=http://downloads.openmicroscopy.org/latest/omero5/server-ice35.zip
wget $SERVER
unzip -q server-ice35.zip
ln -s OMERO.server-*/ OMERO.server
OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
OMERO.server/bin/omero config set omero.db.name "$OMERO_DB_NAME"
OMERO.server/bin/omero config set omero.db.user "$OMERO_DB_USER"
OMERO.server/bin/omero config set omero.db.pass "$OMERO_DB_PASS"
OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS"
psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < OMERO.server/db.sql
# This is the default in 5.2 so could be left unset
OMERO.server/bin/omero config set omero.web.application_server wsgi-tcp
OMERO.server/bin/omero web config nginx --http "$OMERO_WEB_PORT" > OMERO.server/nginx.conf.tmp
To Deploy OMERO.web, you can use either Nginx or Apache. Follow the steps to install your chosen web server.
The following steps are run as root.
Install Nginx, copy the Nginx OMERO configuration file into the Nginx configuration directory, and disable the default configuration:
#!/bin/bash
apt-get -y install nginx
pip install "gunicorn>=19.3"
# See setup_omero*.sh for the nginx config file creation
cp ~omero/OMERO.server/nginx.conf.tmp /etc/nginx/sites-available/omero-web
rm /etc/nginx/sites-enabled/default
ln -s /etc/nginx/sites-available/omero-web /etc/nginx/sites-enabled/
service nginx start
As the omero system user, configure OMERO.web:
#!/bin/bash
set -e -u -x
source settings.env
OMERO.server/bin/omero config set omero.web.application_server wsgi
OMERO.server/bin/omero web config apache24 --http "$OMERO_WEB_PORT" > OMERO.server/apache.conf.tmp
OMERO.server/bin/omero web syncmedia
The following steps are run as root.
Install Apache 2.4:
apt-get -y install apache2 libapache2-mod-wsgi
Copy the Apache OMERO configuration file into the Apache configuration directory, and disable the default configuration:
cp ~omero/OMERO.server/apache.conf.tmp /etc/apache2/sites-available/omero-web.conf
a2dissite 000-default.conf
a2ensite omero-web.conf
service apache2 start
Note
The default value set for the WSGISocketPrefix directive in apache.conf.tmp needs to be modified:
#see https://code.google.com/p/modwsgi/wiki/ConfigurationIssues
WSGISocketPrefix run/wsgi
# Use this on Ubuntu/Debian systems:
# WSGISocketPrefix /var/run/wsgi
The following steps are run as the omero system user.
OMERO should now be set up. To start the server run:
OMERO.server/bin/omero admin start
To start the OMERO.web client run:
OMERO.server/bin/omero web start
Nginx or Apache should already be running so you should be able to log in as the OMERO root user by going to http://localhost/ in your web browser.
In addition some example init.d scripts are available should you wish to start OMERO and OMERO.web automatically:
#!/bin/bash
cp omero-init.d /etc/init.d/omero
chmod a+x /etc/init.d/omero
cp omero-web-init.d /etc/init.d/omero-web
chmod a+x /etc/init.d/omero-web
update-rc.d -f omero remove
update-rc.d -f omero defaults 98 02
update-rc.d -f omero-web remove
update-rc.d -f omero-web defaults 98 02
The following steps are run as root.
If multiple users have access to the machine running OMERO you should restrict access to OMERO.server’s configuration and runtime directories, and optionally the OMERO data directory:
#!/bin/bash
set -e -u -x
source settings.env
chmod go-rwx ~omero/OMERO.server/etc ~omero/OMERO.server/var
# Optionally restrict accesss to the OMERO data directory
#chmod go-rwx "$OMERO_DATA_DIR"
The following steps are run as root.
The default OMERO.web session handler uses temporary files to store sessions which should be deleted at regular intervals, for instance by creating a cron job:
#!/bin/sh
OMERO_USER=omero
OMERO_SERVER=/home/omero/OMERO.server
su - ${OMERO_USER} -c "${OMERO_SERVER}/bin/omero web clearsessions"
Copy this script into the appropriate location:
#!/bin/bash
cp omero-web-cron /etc/cron.daily/omero-web
chmod a+x /etc/cron.daily/omero-web