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.
This section covers the installation of OMERO.server on UNIX and UNIX-like platforms. This includes all BSD, Linux and Mac OS X systems. Depending upon which platform you are using, you may find a more specific walk-through listed below.
See also
Installation will require:
Note
If you are unsure of what it means to have a “root” level account, or if you are generally having issues with the various users/passwords described in this install guide, please see Which user account and password do I use where?.
The installation and configuration of the prerequisite applications are mostly outside the scope of this document. For Linux distributions, use of the default package manager is recommended. For BSD systems, the ports system provides all the prerequisites. For MacOS X, Homebrew is recommended. This guide provides the package names to install for a number of contemporary systems. However, the names and versions provided vary between releases. Please do check for similar packages if the one documented here is not available for your system as it may be provided under an alternative name. “Debian” refers to Debian and derivative distributions such as Ubuntu. “RedHat” refers to RedHat and related distributions such as CentOS, Fedora and Scientific Linux.
For Ubuntu you need to enable the universe repository. This should be enabled by default. If not enabled, it may be enabled by editing /etc/apt/sources.list directly, in which case the entries may already exist but are commented out, or by using Synaptic (10.04 and 10.10) or Ubuntu Software Center (11.04 onwards). Update your package lists to ensure that you get the latest packages:
$ sudo apt-get update
Install packages by running:
$ sudo apt-get install package
where package is the package name to install.
The following subsections cover the details for each package, in the order recommended for installation.
If possible, install one of the following packages:
| System | Package |
|---|---|
| BSD Ports | java/openjdk7 |
| Debian | openjdk-7-jre |
| Homebrew | N/A (install Oracle Java) |
| RedHat | java-1.8.0-openjdk |
OMERO works with the OpenJDK JRE provided by most systems, or with Oracle Java. Version 1.7 or later is required.
Your system may already provide a suitable JRE, in which case no extra steps are necessary. Linux distributions usually provide OpenJDK, and older MacOS X versions have Java installed by default. Oracle Java is no longer provided by BSD or Linux distributions for licensing reasons. If your system does not have Java available, for example on newer MacOS X versions, or the provided version is too old, Oracle Java may be downloaded from the Oracle website.
Warning
Security
Installing Oracle Java outside the system’s package manager will leave your system without regular distribution-supplied security updates, and so is not recommended.
To check which version of Java is currently available:
$ which java
/usr/bin/java
$ java -version
java version "1.7.0_51"
Java(TM) SE Runtime Environment (build 1.7.0_51-b13)
Java HotSpot(TM) 64-Bit Server VM (build 24.51-b03, mixed mode)
Check you have Python (and check its version) by running:
$ python --version
Python 2.7.10
Note
OMERO does not currently support Python 3; you must use 2.7.
The following Python packages are required:
| Package | Functionality | Downloads |
|---|---|---|
| Django (1.8) [1] | OMERO.web | Django page |
| Pillow [2] | OMERO.web and Figure Export | Pillow page |
| Matplotlib | OMERO.web | Matplotlib page |
| NumPy (1.2.0 or higher) [3] | Scripting | Numpy/Scipy page |
| PyTables (2.1.0 or higher) | OMERO.tables | PyTables page |
| [1] | The currently supported version of the django module used by OMERO.web (1.8) requires Python 2.7. The older version (1.6) will work with Python 2.6 but lacks security support, and is consequently not recommended for production use. Python 2.7 and Django 1.8 are required for security support. |
| [2] | Make sure to have libjpeg installed when building Pillow. We currently do not support version 3.0+. |
| [3] | May already have been installed as a dependency of Matplot Lib. |
Note
Some of these can be ignored if you wish to forego some functionality but we recommend you just install everything. For example, scripting is enabled by default so should not be assumed optional even if you never expect your users to run scripts from the clients.
If possible, install the following packages:
| System | Package |
|---|---|
| BSD Ports | lang/python27 graphics/py-pillow math/py-matplotlib math/py-numpy devel/py-tables science/py-scipy |
| Debian | python2.7 python-pil python-matplotlib python-numpy python-tables python-scipy |
| Homebrew | python pillow numpy matplotlib |
| RedHat | python |
Note
CentOS 6 users should read OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.5 or OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.6 and follow the instructions there to install Python and the required modules.
Note
OMERO 5.2 supports 3.5 and 3.6 on UNIX and UNIX-like platforms. You must install the correct version of OMERO.server (see Downloads).
The Ice version may vary, depending upon the distribution version you are using. The Ice versions in currently supported versions of Debian and Ubuntu are shown in the Ice of the Version requirements page.
Using the latest version of Ice is recommended, where possible. If your package manager provides Ice packages, using these is recommended where possible. Distribution-provided packages often have additional bugfixes which are not present in the upstream releases.
If needed, source and binary packages are available from ZeroC. The latest release is available from the ZeroC website.
Note
CentOS 6 users should read OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.5 or OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.6 and follow the instructions there to install Ice.
Note
ZeroC Ice can always be built from source code for specific platforms if a binary package is not available.
Note
With Ice 3.6, the Python bindings are provided separately. If your package manager does not provide Ice python packages, run pip install zeroc-ice to install the Ice Python bindings. See Using the Python Distribution for further details.
Please install one of apache (and its wsgi module) or nginx and Gunicorn in order to run OMERO.web.
| System | Packages |
|---|---|
| BSD Ports | www/apache24 www/nginx |
| Debian | apache2 libapache2-mod-wsgi nginx |
| Homebrew | nginx |
| RedHat | httpd mod_wsgi nginx |
If you wish to run the “Movie Maker” script, please install mencoder.
| System | Packages |
|---|---|
| BSD Ports | multimedia/mencoder |
| Debian | mencoder |
| Homebrew | mplayer |
| RedHat | mencoder |
Once the above prerequisites have been downloaded, installed and configured appropriately, the OMERO server itself may be installed. You may wish to create a user account solely for the purpose of running the server, and switch to this user for the next steps.
Firstly, a directory needs to be created to contain the server. In this case ~/omero is used as an example:
$ mkdir -p ~/omero
Next, change into this directory:
$ cd ~/omero
The release OMERO.server.zip is available from the OMERO downloads page. Download the version matching the version of Ice installed on your system before continuing.
Installing a development version from source is also possible. See the Installing OMERO from source section for further details. This is not recommended unless you have a specific reason not to use a release version.
Once you have obtained the OMERO.server zip archive matching the version of Ice installed, unpack it:
$ unzip OMERO.server-5.2.8-ice35-byy.zip
If your system does not provide an unzip command by default, install one of the following:
| System | Package |
|---|---|
| BSD Ports | archivers/unzip |
| Debian | unzip |
| Homebrew | unzip |
| RedHat | unzip |
Optionally, give your OMERO software install a short name to save some typing later, to reflect what you set OMERO_PREFIX to in the Environment variables section, below:
$ ln -s OMERO.server-5.2.8-ice35-byy OMERO.server
This will also ease installation of newer versions of the server at a later date, by simply updating the link.
If using distribution-provided packages such as Debian or RPM packages, or via the homebrew or macports package manager, it should not be necessary to set any environment variables. However, if using third-party packages for any required components, several variables may require setting in order for them to function correctly.
Please note that the precise details of these environment variables can change as new versions of software are released.
There are several methods for setting environment variables; which is most appropriate will depend upon how the OMERO server is started. Options include:
If OMERO is started as a service using an init script, a global setting should be preferred. If being started by hand using a particular user, a user-specific configuration file may be more appropriate.
The following environment variables may be configured:
Warning
The OMERO_HOME environment variable is used internally by OMERO. Unless you really know what you are doing, it is strongly recommended that you do not set this variable (see Setting the OMERO_HOME environment variable for details). You can use a different name of your choice instead, indicated by OMERO_PREFIX in this documentation.
After making any needed changes, either source the corresponding file or log back in for them to take effect. Run env to check them.
Note
CentOS 6 users should read OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.5 or OMERO.server installation on CentOS 6 with Python 2.7 and Ice 3.6 and set the needed environment variables as documented.
On most systems, a “postgres” user will be created which has admin privileges, while the UNIX root user itself does not have admin privileges. Therefore it is necessary to either become the postgres user, or use sudo as shown below.
For the purposes of this guide, the following dummy data is used:
Username: db_user
Password: db_password
Database: omero_database
Warning
Security
These dummy values are examples only and should not be used. For a live or public server install these values should be altered to reflect your security requirements—i.e. use your own choice of username and password instead. These should not be the same username and/or password as your Linux/Mac/Windows root user!
You should also consider restricting access to your server machine, but that is outside the scope of this document.
Create a non-superuser database user and record the name and password used. You will need to configure OMERO to use this username and password later on.:
$ sudo -u postgres createuser -P -D -R -S db_user
Enter password for new role: # db_password
Enter it again: # db_password
Create a database for OMERO to reside in:
$ sudo -u postgres createdb -E UTF8 -O db_user omero_database
Check to make sure the database has been created, you have PostgreSQL client authentication correctly set up and the database is owned by the db_user user.
$ psql -h localhost -U db_user -l
Password for user db_user:
List of databases
Name | Owner | Encoding
----------------+----------+-----------
omero_database | db_user | UTF8
postgres | postgres | UTF8
template0 | postgres | UTF8
template1 | postgres | UTF8
(4 rows)
If you have problems, especially with the last step, take a look at OMERO.server and PostgreSQL since the authentication mechanism is probably not properly configured.
Create a directory for the OMERO binary data repository. /OMERO is the default location and should be used unless you explicitly have a reason not to and know what you are doing.
This is not where you want the OMERO application to be installed, it is a separate directory which the OMERO.server will use to store binary data.
You can read more about the OMERO binary repository.
$ sudo mkdir /OMERO
Change the ownership of the directory. /OMERO must either be owned by the user starting the server (it is currently owned by the system root) or that user must have permission to write to the directory. You can find out your username and edit the correct permissions as follows:
$ whoami
omero
$ sudo chown -R omero /OMERO
Optionally, review ~/omero/OMERO.server/etc/omero.properties, which contains all default settings. Do not edit this file—it is for reference only. Any configuration settings you would like to change can be changed in the next step. Alternatively, you can view a parsed version of the file under Configuration properties glossary or parse it yourself with omero config parse.
Change any settings that are necessary using omero config, including the name and/or password for the ‘db_user’ database user you chose above or the database name if it is not “omero_database”. (Quotes are only necessary if the value could be misinterpreted by the shell. See link)
$ cd ~/omero/OMERO.server
$ bin/omero config set omero.db.name 'omero_database'
$ bin/omero config set omero.db.user 'db_user'
$ bin/omero config set omero.db.pass 'db_password'
You can also check the values that have been set using:
$ cd ~/omero/OMERO.server
$ bin/omero config get
If you have chosen a non-standard OMERO binary repository location above, be sure to configure the omero.data.dir property. For example, to use /srv/omero:
$ omero config set omero.data.dir /srv/omero
Create the OMERO database initialization script. You will need to provide a password for the newly created OMERO root user, either by using the --password argument or by entering it when prompted. Note that this password is for the root user of the OMERO.server, and is not related to the root system user or a PostgreSQL user role.
$ cd ~/omero/OMERO.server
$ bin/omero db script --password omero_root_password
Using OMERO5.2 for version
Using 0 for patch
Using password from commandline
Saving to /home/omero/OMERO5.2__0.sql
Warning
Security
For illustrative purposes, the default password for the OMERO root user is shown as omero_root_password. However, you should not use this default values for your installation, but use your own choice of password instead. This should not be the same password as your Linux/Mac/Windows root user or the database user!
Initialize your database with the script.
$ psql -h localhost -U db_user omero_database < OMERO5.2__0.sql
At this point you should see some output from PostgreSQL as it installs the schema for new OMERO database.
Before starting the OMERO.server, run the OMERO diagnostics script to check that all of the settings are correct, e.g.
$ bin/omero admin diagnostics
You can now start the server using:
$ bin/omero admin start
Creating var/master
Initializing var/log
Creating var/registry
No descriptor given. Using etc/grid/default.xml
If multiple users have access to the system running OMERO you should restrict access to the OMERO.server/etc and OMERO.server/var directories, for example by changing the permissions on them:
$ chmod 700 ~/omero/OMERO.server/etc ~/omero/OMERO.server/var
You should also consider restricting access to the OMERO data repository. The required permissions will depend on whether you are using Advanced import scenarios.
Test that you can log in as “root”, either with the OMERO.insight client or on the command-line:
$ bin/omero login
Server: [localhost]
Username: [root]
Password: # omero_root_password
You will be prompted for an OMERO username and password. Use the username and password set when running bin/omero db script.
If your users are going to be importing many files in one go, for example multiple plates, you should make sure you set the maximum number of open files to a sensible level (i.e. at least 8K for production systems, 16K for bigger machines). See Too many open files for more information.
The OMERO server starts a number of Java services. Memory settings for these are calculated on a system-by-system basis. An attempt has been made to have usable settings out of the box, but if you can afford to provide OMERO with more memory, it will certainly improve your overall performance. See Memory configuration on how to tune the JVM.
In order to deploy OMERO.web in a production environment such as Apache or Nginx please follow the instructions under OMERO.web deployment.
Note
The internal Django webserver can be used for evaluation and development. In this case please follow the instructions under OMERO.web deployment for developers.
OMERO has a facility to create AVI/MPEG Movies from images. The page OMERO.movie details how to enable it.
One of your first steps after putting your OMERO server into production should be deciding on when and how you are going to backup your database and binary data. Please do not omit this step.
It is also now recommended that you read the Server security and firewalls page to get a good idea as to what you need to do to get OMERO clients speaking to your newly installed OMERO.server in accordance with your institution or company’s security policy.
Once you have the base server running, you may want to try enabling some of the advanced features such as OMERO.dropbox or LDAP authentication. If you have Flex data, you may want to watch the HCS configuration screencast. See the Feature list for more advanced features you may want to use, and Configuration properties glossary on how to get the most out of your server.
My OMERO install doesn’t work! What do I do now? Examine the Troubleshooting OMERO page and if all else fails post a message to our ome-users mailing list discussed on the Community support page. Especially the Server fails to start and Remote clients cannot connect to OMERO installation sections are a good starting point.
If you want help with your server installation, please include the output of the diagnostics command:
$ bin/omero admin diagnostics
================================================================================
OMERO Diagnostics 5.2.8
================================================================================
Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.7.9 (/usr/bin/python)
Commands: icegridnode --version 3.5.1 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.5.1 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.5 (/usr/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 30324, enabled)
Server: DropBox active (pid = 30343, enabled)
Server: FileServer active (pid = 30345, enabled)
Server: Indexer-0 active (pid = 30348, enabled)
Server: MonitorServer active (pid = 30351, enabled)
Server: OMERO.Glacier2 active (pid = 30353, enabled)
Server: OMERO.IceStorm active (pid = 30376, enabled)
Server: PixelData-0 active (pid = 30393, enabled)
Server: Processor-0 active (pid = 30394, enabled)
Server: Tables-0 inactive (disabled)
Server: TestDropBox inactive (enabled)
OMERO: SSL port 4064
OMERO: TCP port 4063
Log dir: /home/omero/OMERO.server-5.0.1-ice35-b21/var/log exists
Log files: Blitz-0.log 3.0 MB errors=0 warnings=9
Log files: DropBox.log 4.0 KB errors=0 warnings=1
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 10.0 KB errors=0 warnings=5
Log files: MonitorServer.log 2.0 KB
Log files: OMEROweb.log 642.0 KB errors=0 warnings=1
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 7.0 KB errors=0 warnings=4
Log files: Processor-0.log 2.0 KB errors=0 warnings=1
Log files: Tables-0.log n/a
Log files: TestDropBox.log n/a
Log files: master.err 0.0 KB errors=2 warnings=0
Log files: master.out 0.0 KB
Log files: Total size 3.83 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir: '/OMERO' Exists? True Is writable? True
OMERO temp dir: '/home/omero/tmp' Exists? True Is writable? True (Size: 0)
JVM settings: Blitz-${index} -Xmx621m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx414m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx621m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx414m -XX:MaxPermSize=512m -XX:+IgnoreUnrecognizedVMOptions
OMERO.web status... You are deploying OMERO.web using apache and mod_wsgi. Cannot check status.
Django version: 1.8.7
Your OMERO.server installation will check for updates each time it is started from the Open Microscopy Environment update server. If you wish to disable this functionality you should do so now as outlined on the OMERO upgrade checks page.