OMERO.server installation on CentOS 6 with Python 2.7

This installation walkthrough should be read in conjunction with OMERO.server installation overview and Setting up OMERO.web.

Running OMERO on CentOS 6 has a number of special requirements which deviate from the standard installation instructions. The instructions below will set up Python 2.7 and Ice 3.6 on CentOS 6. We tested the installation with Python 2.7 from IUS and used a virtual environment to install the various dependencies required to install an OMERO.server. It is also possible to use SCL Python (for example walkthrough_centos6_py27.sh) but such solution could have potential side effects.

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

Setting up

Python 2.7

CentOS 6 provides Python 2.6. However, OMERO.web requires Python 2.7 in order to use Django 1.8. While Django 1.6 may be used with Python 2.6, this version of Django no longer has security support. In consequence, it is necessary to upgrade to Python 2.7 in order to obtain Django security updates, which are required for a production deployment.

Ice 3.6

With Ice 3.6, the Python bindings are provided separately. This allows to install the RPM packages provided by ZeroC for CentOS 6. Then run pip install zeroc-ice to install the Ice Python bindings if your package manager does not provide the Ice python packages. See Using the Python Distribution for further details.

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:

# epel-release will be pulled as a dependency
yum -y install https://centos6.iuscommunity.org/ius-release.rpm

# installed for convenience
yum -y install unzip wget tar bc

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

# install dependencies

yum -y install \
	python27 \
	python27-devel \
	python27-yaml \
	python27-jinja2 \
	hdf5-devel

yum -y install libjpeg-devel zlib-devel

# install pip and virtualenv using Python 2.6 
yum -y install python-pip

pip install --upgrade virtualenv

#if virtualenv is not installed (unlikely)
#yum -y install python27-pip
#pip2.7 install virtualenv

# TODO: this installs a lot of unecessary packages:
yum -y groupinstall "Development Tools"

export PYTHONWARNINGS="ignore:Unverified HTTPS request"

To install Ice 3.6:

cd /etc/yum.repos.d
wget https://zeroc.com/download/rpm/zeroc-ice-el6.repo

yum -y install gcc-c++
yum -y install db53 db53-utils
yum -y install ice-all-runtime ice-all-devel

yum -y install openssl-devel bzip2-devel expat-devel

virtualenv -p /usr/bin/python2.7 /home/omero/omeroenv
set +u
source /home/omero/omeroenv/bin/activate
set -u

/home/omero/omeroenv/bin/pip2.7 install "zeroc-ice>3.5,<3.7"

deactivate

To install PostgreSQL 9.6:

# install Postgres
# Postgres, reconfigure to allow TCP connections
yum -y install http://yum.postgresql.org/9.6/redhat/rhel-6-x86_64/pgdg-centos96-9.6-3.noarch.rpm
yum -y install postgresql96-server postgresql96

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

The remaining dependencies will be installed in a virtual environment:

# Install the OMERO dependencies in a virtual environment
# Create virtual env.
# -p only required if virtualenv has been installed with python 2.6

virtualenv -p /usr/bin/python2.7 /home/omero/omeroenv
set +u
source /home/omero/omeroenv/bin/activate
set -u
/home/omero/omeroenv/bin/pip install --upgrade pip

/home/omero/omeroenv/bin/pip2.7 install -r requirements_centos6_py27_ius.txt

deactivate

See requirements_centos6_py27_ius.txt

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

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:

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 settings will need adding to your OMERO startup script or to the omero user’s environment (for example in a shell startup script). Add the absolute path to the bin directory of the virtual environment /home/omero/omeroenv to the PATH variable:

echo "export PATH=\"/home/omero/omeroenv/bin:$PATH\"" >> ~omero/.bashrc

These settings will enable Python 2.7, and set the necessary environment variables for Ice 3.6 to work.

Install 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=http://downloads.openmicroscopy.org/latest/omero5.3/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

Installing and running OMERO.web

OMERO.web is deployed using Nginx see OMERO.web WSGI deployment.

The following steps are run as root.

Install the latest stable version of Nginx, install the requirements to run OMERO.web in the virtual environment, deactivate it and copy the Nginx OMERO configuration file into the Nginx configuration directory, and disable the default configuration:

cat << EOF > /etc/yum.repos.d/nginx.repo
[nginx]
name=nginx repo
baseurl=http://nginx.org/packages/centos/\$releasever/\$basearch/
gpgcheck=0
enabled=1
EOF

#install nginx
yum -y install nginx

virtualenv -p /usr/bin/python2.7 /home/omero/omeroenv
set +u
source /home/omero/omeroenv/bin/activate
set -u

# Install OMERO.web requirements
if [ "$ICEVER" = "ice36" ]; then
file=~omero/OMERO.server/share/web/requirements-py27-all.txt
else
file=~omero/OMERO.server/share/web/requirements-py27-all-ice35.txt
fi
/home/omero/omeroenv/bin/pip2.7 install -r $file
#start-configure-nginx: As the omero system user, configure OMERO.web
OMERO.server/bin/omero config set omero.web.application_server wsgi-tcp
OMERO.server/bin/omero web config nginx --http "$OMERO_WEB_PORT" > OMERO.server/nginx.conf.tmp
#end-configure-nginx
mv /etc/nginx/conf.d/default.conf /etc/nginx/conf.d/default.disabled
cp ~omero/OMERO.server/nginx.conf.tmp /etc/nginx/conf.d/omero-web.conf

service nginx start

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

Please read the SELinux section below.

In addition an init.d script is available should you wish to start OMERO automatically.

omero-init.d

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/OMERO.server/etc ~omero/OMERO.server/var

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

Regular tasks

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:

OMERO_USER=omero
OMERO_SERVER=/home/omero/OMERO.server
su - ${OMERO_USER} -c "${OMERO_SERVER}/bin/omero web clearsessions"

Copy the following commands into the appropriate location:

cp omero-web-cron /etc/cron.daily/omero-web
chmod a+x /etc/cron.daily/omero-web

omero-web-cron

SELinux

The following steps are run as root.

If you are running a system with SELinux enabled (it is enabled by default on CentOS 6) and are unable to access OMERO.web you may need to adjust the security policy:

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

Installing Web apps

The following steps are run as root.

It is possible to add Web applications to OMERO. If your app required some extra Python packages installed using pip, those packages should be also installed in the virtual environment. For example, OMERO.figure requires reportlab and markdown:

virtualenv -p /usr/bin/python2.7 /home/omero/omeroenv
source /home/omero/omeroenv/bin/activate
/home/omero/omeroenv/bin/pip2.7 install reportlab markdown