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:
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="$OMERO_DB_PASS"
Installing prerequisites¶
The following steps are run as root.
Install Java 1.8, Ice 3.6 and PostgreSQL 9.6:
To install Java 1.8 and other dependencies:
yum -y install epel-release
# installed for convenience
yum -y install unzip wget bc
# install Java
yum -y install java-1.8.0-openjdk
# install dependencies
yum -y install python-{pip,devel,virtualenv,yaml,jinja2,tables}
To install dependencies required by OMERO core scripts:
yum -y install python-pillow numpy
To install Ice 3.6:
curl -sL https://zeroc.com/download/Ice/3.6/el7/zeroc-ice3.6.repo > \
/etc/yum.repos.d/zeroc-ice3.6.repo
yum -y install gcc-c++
yum -y install libdb-utils
yum -y install openssl-devel bzip2-devel
yum -y install ice-all-runtime
pip install "zeroc-ice>3.5,<3.7"
To install PostgreSQL 9.6:
# Postgres, reconfigure to allow TCP connections
yum -y install http://yum.postgresql.org/9.6/redhat/rhel-7-x86_64/pgdg-centos96-9.6-3.noarch.rpm
yum -y install postgresql96-server postgresql96
PGSETUP_INITDB_OPTIONS=--encoding=UTF8 /usr/pgsql-9.6/bin/postgresql96-setup initdb
sed -i.bak -re 's/^(host.*)ident/\1md5/' /var/lib/pgsql/9.6/data/pg_hba.conf
systemctl start postgresql-9.6.service
systemctl enable postgresql-9.6.service
Create an omero system user, and a directory for the OMERO repository:
useradd -m omero
# Give a password to the omero user
# e.g. passwd omero
chmod a+X ~omero
mkdir -p "$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.
Install server-ice36.zip:
cd ~omero
SERVER=https://downloads.openmicroscopy.org/latest/omero5/server-ice36.zip
wget $SERVER -O OMERO.server-ice36.zip
unzip -q OMERO.server*
Configure:
ln -s OMERO.server-*/ OMERO.server
OMERO.server/bin/omero config set omero.data.dir "$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
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"
