OMERO.server installation on CentOS 7

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 administration. 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.

This guide describes how to install the recommended versions, not all the supported versions. This should be read in conjunction with Version requirements.

This guide does not describe how to install OMERO.web. To deploy OMERO.web separately from OMERO.server (recommended), please read OMERO.web installation separately from OMERO.server on CentOS 7 and IcePy 3.6 or to deploy with OMERO.server OMERO.web installation with OMERO.server on CentOS 7 and IcePy 3.6

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 settings.env:




Installing prerequisites

The following steps are run as root.

Install Java 1.8, Ice 3.6 and PostgreSQL 9.6:

To install Java 1.8 and other dependencies:

yum -y install epel-release

# installed for convenience
yum -y install unzip wget bc

# install Java
yum -y install java-1.8.0-openjdk

# install dependencies

yum -y install python-{pip,devel,virtualenv,yaml,jinja2,tables}
pip install --upgrade pip

To install dependencies required by OMERO core scripts:

yum -y install python-pillow numpy

To install Ice 3.6:

curl -sL > \
yum -y install gcc-c++
yum -y install libdb-utils
yum -y install openssl-devel bzip2-devel

yum -y install ice-all-runtime

pip install "zeroc-ice>3.5,<3.7"

To install PostgreSQL 9.6:

# install Postgres
# Postgres, reconfigure to allow TCP connections
yum -y install
yum -y install postgresql96-server postgresql96

PGSETUP_INITDB_OPTIONS=--encoding=UTF8 /usr/pgsql-9.6/bin/postgresql96-setup initdb

sed -i.bak -re 's/^(host.*)ident/\1md5/' /var/lib/pgsql/9.6/data/pg_hba.conf
systemctl start postgresql-9.6.service

systemctl enable postgresql-9.6.service

Create an omero system user, and a directory for the OMERO repository:

useradd -m omero
# Give a password to the omero user
# e.g. passwd 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:

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

Installing OMERO.server

The following steps are run as the omero system user.

Download, unzip and configure OMERO. 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.

You will need to install the server corresponding to your Ice version.


cd ~omero
wget $SERVER -O
unzip -q OMERO.server*


ln -s OMERO.server-*/ OMERO.server
OMERO.server/bin/omero config set "$OMERO_DATA_DIR"
OMERO.server/bin/omero config set "$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

Running OMERO.server

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

In addition omero-systemd.service is available should you wish to start OMERO automatically.

Securing OMERO

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:

chmod go-rwx OMERO.server/etc OMERO.server/var

# Optionally restrict access to the OMERO data directory
# chmod go-rwx "$OMERO_DATA_DIR"