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 CentOS 7, 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 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="$OMERO_DB_PASS"
The following steps are run as root.
Install Ice, Java, PostgreSQL:
yum -y install epel-release
curl -o /etc/yum.repos.d/zeroc-ice-el7.repo \
http://download.zeroc.com/Ice/3.5/el7/zeroc-ice-el7.repo
yum -y install \
unzip \
wget \
java-1.8.0-openjdk \
ice ice-python ice-servers
yum -y install \
python-pip python-devel python-virtualenv \
numpy scipy python-matplotlib python-tables
# upgrade pip to run 7.1.2
pip install --upgrade pip
# install Pillow via pip
yum -y install \
zlib-devel \
libjpeg-devel \
gcc
# Cap Pillow version due to a limitation in OMERO.figure with v3.0.0
pip install 'Pillow<3.0'
# Django
pip install 'Django>=1.8,<1.9'
# Postgres, reconfigure to allow TCP connections
yum -y install http://yum.postgresql.org/9.4/redhat/rhel-7-x86_64/pgdg-centos94-9.4-2.noarch.rpm
yum -y install postgresql94-server postgresql94
PGSETUP_INITDB_OPTIONS=--encoding=UTF8 /usr/pgsql-9.4/bin/postgresql94-setup initdb
sed -i.bak -re 's/^(host.*)ident/\1md5/' /var/lib/pgsql/9.4/data/pg_hba.conf
systemctl start postgresql-9.4.service
systemctl enable postgresql-9.4.service
Create an omero system user, and a directory for the OMERO repository:
#!/bin/bash
useradd -m omero
chmod a+X ~omero
mkdir -p "$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 "$OMERO_WEB_PORT" > OMERO.server/nginx.conf.tmp
To Deploy OMERO.web, you can use either Nginx or Apache. Follow the steps to install your chosen web server.
The following steps are run as root.
Install Nginx, copy the Nginx OMERO configuration file into the Nginx configuration directory, and disable the default configuration:
#!/bin/bash
yum -y --enablerepo=cr install nginx python-gunicorn
# See setup_omero*.sh for the nginx config file creation
sed -i.bak -re 's/( default_server.*)/; #\1/' /etc/nginx/nginx.conf
cp ~omero/OMERO.server/nginx.conf.tmp /etc/nginx/conf.d/omero-web.conf
systemctl enable nginx
systemctl start nginx
bash -eux setup_centos_selinux.sh
As the omero system user, configure OMERO.web:
#!/bin/bash
set -e -u -x
source settings.env
OMERO.server/bin/omero config set omero.web.application_server wsgi
OMERO.server/bin/omero web config apache24 --http "$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:
yum -y install httpd mod_wsgi
Copy the Apache OMERO configuration file into the Apache configuration directory:
cp ~omero/OMERO.server/apache.conf.tmp /etc/httpd/conf.d/omero-web.conf
rm -rf /run/httpd/* /tmp/httpd*
systemctl enable httpd.service
systemctl start httpd
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. Please read the SELinux section below.
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
chkconfig --del omero
chkconfig --add omero
chkconfig --del omero-web
chkconfig --add omero-web
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
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:
#!/bin/bash
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