# OMERO.server installation on Ubuntu 22.04

This is an example walkthrough for installing OMERO on Ubuntu 22.04, using a dedicated local system user. 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 will install Python 3.10. Since 5.6, a new `OMERODIR` variable is used, you should first unset `OMERO_HOME` (if set) before beginning the installation process.

This guide describes how to install using the recommended versions for Java, Ice, PostgreSQL. This should be read in conjunction with Version requirements.

This guide does not describe how to install OMERO.web. To deploy OMERO.web, please read OMERO.web installation on Ubuntu 22.04 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 we will use the omero-server system user and the main OMERO configuration options have been defined as environment variables. When following this walkthrough you can either use your own values, or alternatively create `settings.env` for example under `/tmp` e.g. `/tmp/settings.env` containing the variables below and source it when required:

    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

    export OMERO_DB_USER OMERO_DB_PASS OMERO_DB_NAME OMERO_ROOT_PASS OMERO_DATA_DIR

    export PGPASSWORD="$OMERO_DB_PASS"

    # Location of the OMERO.server
    export OMERODIR=/opt/omero/server/OMERO.server

    # Location of the virtual environment for omero-py
    VENV_SERVER=/opt/omero/server/venv3

    export ICE_HOME=/opt/ice-3.6.5

    export PATH=$ICE_HOME/bin:$VENV_SERVER/bin:$PATH

## Installing prerequisites

The following steps are run as root.

Install Java 11, Ice 3.6.5 and PostgreSQL 14:

To install Java 11 and other dependencies:

    apt-get update

    apt-get -y install unzip wget bc

    # to be installed if daily cron tasks are configured
    apt-get -y install cron

    # install Java
    apt-get update -q
    apt-get install -y openjdk-11-jre

    # install dependencies

    # start-add-dependencies
    apt-get -y install \
        unzip \
        wget \
        python3 \
        python3-venv
    # end-add-dependencies

To install Ice 3.6.5:

    apt-get update && \
    apt-get install -y -q \
    db5.3-util \
    bzip2 \
    libdb++ \
    libexpat1 \
    libmcpp0 \
    openssl \
    mcpp \
    zlib1g

    cd /tmp
    wget -q https://github.com/glencoesoftware/zeroc-ice-ubuntu2204-x86_64/releases/download/20221004/Ice-3.6.5-ubuntu2204-x86_64.tar.gz
    tar xf Ice-3.6.5-ubuntu2204-x86_64.tar.gz
    mv Ice-3.6.5 /opt/ice-3.6.5
    echo /opt/ice-3.6.5/lib64 > /etc/ld.so.conf.d/ice-x86_64.conf
    ldconfig

To make Ice available to all users and activate the virtual environment, set the following in `/etc/profile`:

    # Environment file for OMERO

    export ICE_HOME=/opt/ice-3.6.5
    export PATH="$ICE_HOME/bin:$PATH"
    #Remove commented out export below if Ice is not set globally accessible
    #export LD_LIBRARY_PATH="$ICE_HOME/lib64:$ICE_HOME/lib:$LD_LIBRARY_PATH"
    export SLICEPATH="$ICE_HOME/slice"

and add the virtual environment to `PATH`:

    VENV_SERVER=/opt/omero/server/venv3

    export ICE_HOME=/opt/ice-3.6.5

    export PATH=$ICE_HOME/bin:$VENV_SERVER/bin:$PATH

To install PostgreSQL:

    apt-get install -y curl ca-certificates
    install -d /usr/share/postgresql-common/pgdg
    curl -o /usr/share/postgresql-common/pgdg/apt.postgresql.org.asc --fail https://www.postgresql.org/media/keys/ACCC4CF8.asc
    sh -c 'echo "deb [signed-by=/usr/share/postgresql-common/pgdg/apt.postgresql.org.asc] https://apt.postgresql.org/pub/repos/apt jammy-pgdg main" > /etc/apt/sources.list.d/pgdg.list'

    apt-get update
    apt-get -y install postgresql-15
    service postgresql start

Create a local omero-server system user, and a directory for the OMERO repository:

    useradd -mr omero-server
    # Give a password to the omero user
    # e.g. passwd omero-server
    chmod a+X ~omero-server

    mkdir -p "$OMERO_DATA_DIR"
    chown omero-server "$OMERO_DATA_DIR"

Make the `settings.env` available to the omero-server system user by copying in to the user home directory. The file will need to be sourced each time you switch user. You could add `. ~/settings.env` to the omero-server system user `bash` profile.

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 step is run as root.

We recommend to create a virtual environment and install the Ice Python binding and the dependencies required by the server using `pip`:

    # Create a virtual env
    python3 -mvenv $VENV_SERVER

    # Upgrade pip
    $VENV_SERVER/bin/pip install --upgrade pip

    # Install the Ice Python binding
    $VENV_SERVER/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-ubuntu2204-x86_64/releases/download/20221004/zeroc_ice-3.6.5-cp310-cp310-linux_x86_64.whl

    # Install server dependencies
    $VENV_SERVER/bin/pip install omero-server

Download and unzip OMERO.server:

    cd /opt/omero/server
    SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip
    wget -q $SERVER -O OMERO.server-ice36.zip
    unzip -q OMERO.server*

Change the ownership of the OMERO.server directory and create a symlink:

    # change ownership of the folder
    chown -R omero-server OMERO.server-*
    ln -s OMERO.server-*/ OMERO.server

## Configuring OMERO.server

The following steps are run as the omero-server system user. (`su - omero-server`)

The variable `OMERODIR` set in `settings.env` above must point to the location where OMERO.server is installed. e.g. `OMERODIR=/path_to_omero_server/OMERO.server`.

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.

Configure the database and the location of the data directory:

    omero config set omero.data.dir "$OMERO_DATA_DIR"
    omero config set omero.db.name "$OMERO_DB_NAME"
    omero config set omero.db.user "$OMERO_DB_USER"
    omero config set omero.db.pass "$OMERO_DB_PASS"
    omero db script -f $OMERODIR/db.sql --password "$OMERO_ROOT_PASS"
    psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < $OMERODIR/db.sql

Weaker ciphers like ADH are disabled by default in new versions of OpenSSL and TLS versions 1.0 and 1.1 have been dropped from JDK packages. In order to connect to an OMERO.server using any OMERO clients e.g. the Java Desktop client, the OMERO.web client or the CLI and import data, you need to generate self-signed certificates after installing the omero-certificates package.

    omero certificates

See also Client Server SSL verification.

## Running OMERO.server

The following steps are run as the omero-server system user. (`su - omero-server`)

OMERO should now be set up. To start the server run:

    omero admin start

Should you wish to start OMERO automatically, a init.d file could be created. An example `omero-server-init.d` is available.

Copy the `init.d` file and configure the service:

    cp omero-server-init.d /etc/init.d/omero-server
    chmod a+x /etc/init.d/omero-server

    update-rc.d -f omero-server remove
    update-rc.d -f omero-server defaults 98 02

You can then start up the service by running:

    service omero-server start

## 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 $OMERODIR/etc $OMERODIR/var

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