Note

This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.6¶

This installation walkthrough should be read in conjunction with OMERO.server installation and OMERO.web deployment.

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.

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 9.4:

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 \
	libjpeg-devel \
	libpng-devel \
	libtiff-devel \
	hdf5-devel \
	zlib-devel \
	freetype-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 9.4:

# install Postgres
# Postgres, reconfigure to allow TCP connections
yum -y install http://yum.postgresql.org/9.4/redhat/rhel-6-x86_64/pgdg-centos94-9.4-2.noarch.rpm
yum -y install postgresql94-server postgresql94

service postgresql-9.4 initdb
sed -i.bak -re 's/^(host.*)ident/\1md5/' /var/lib/pgsql/9.4/data/pg_hba.conf
chkconfig postgresql-9.4 on
service postgresql-9.4 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

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

Create a database user and initialize a new database for OMERO. As postgres who is the admin for a PostgreSQL installation, run:

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/omero5.2/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 a web server¶

To deploy OMERO.web, you can use either Nginx or Apache. Follow the steps to install your chosen web server.

Nginx¶

The following steps are run as root.

Install Nginx 1.8, 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
file=~omero/OMERO.server/share/web/requirements-py27-nginx.txt
/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

Apache (deprecated)¶

As the omero system user, configure OMERO.web by running the following commands:

OMERO.server/bin/omero config set omero.web.application_server wsgi
OMERO.server/bin/omero web config apache --http "$OMERO_WEB_PORT" > OMERO.server/apache.conf.tmp
OMERO.server/bin/omero web syncmedia

The following steps are run as root.

The version of Apache installed is 2.2, see the note below if you wish to use version 2.4.

Install Apache 2.2, install the requirements to run OMERO.web in the virtual environment, deactivate it and add the path to the virtual environment python to the python-path parameter of the WSGIDaemonProcess directive:

#install Apache 2.2
yum -y install httpd

# install mod_wsgi compiled against 2.7
yum -y install python27-mod_wsgi

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

# Install OMERO.web requirements
file=~omero/OMERO.server/share/web/requirements-py27-apache.txt
# introduced in 5.2.0
if [ -f $file ]; then
	/home/omero/omeroenv/bin/pip2.7 install -r $file
fi
deactivate


# Add virtual env python to the python-path parameter of the WSGIDaemonProcess directive
sed -i 's/\(python-path\=\)/\1\/home\/omero\/omeroenv\/lib64\/python2.7\/site-packages:/' ~omero/OMERO.server/apache.conf.tmp

cp ~omero/OMERO.server/apache.conf.tmp /etc/httpd/conf.d/omero-web.conf

chkconfig httpd on
service httpd start

Note

If you wish to use Apache 2.4 with mod_wsgi, see omero-install for a possible solution.

Running OMERO¶

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

If you deploy with Nginx, to start the OMERO.web client run:

OMERO.server/bin/omero web start

The last command is not necessary if you deploy with Apache.

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:

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

omero-init.d

omero-web-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

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OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.6¶

Setting up¶

Python 2.7¶

Ice 3.6¶

Installing prerequisites¶

Install OMERO.server¶

Installing a web server¶

Nginx¶

Apache (deprecated)¶

Running OMERO¶

Securing OMERO¶

Regular tasks¶

SELinux¶

Installing Web apps¶

Navigation

Page Contents

OMERO

Previous topic

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This Page

OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.6¶

Setting up¶

Python 2.7¶

Ice 3.6¶

Installing prerequisites¶

Install OMERO.server¶

Installing a web server¶

Nginx¶

Apache (deprecated)¶

Running OMERO¶

Securing OMERO¶

Regular tasks¶

SELinux¶

Installing Web apps¶

Navigation