OMERO.server installation on OS X with Homebrew

Overview

This walkthrough demonstrates how to install OMERO on a clean Mac OS X system (10.9 or later). Dependencies are installed with Homebrew. The OMERO.server can be downloaded as a pre-built zip, or built from the source code. It is aimed at developers since typically MacOS X is not suited for serious server deployment.

Prerequisites

Xcode

Homebrew requires the latest version of Xcode. Install Xcode and the Command Line Tools for Xcode from the App Store. If you have already installed it, make sure all the latest updates are installed.

Homebrew

Homebrew will install all packages under /usr/local. See also: Installation instructions on the Homebrew wiki.

Install Homebrew using the following command in terminal:

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Java

Oracle Java may be downloaded from the Oracle website.

After installing JDK 7 or JDK 8, check your installation works by running:

$ java -version
java version "1.8.0_51"
Java(TM) SE Runtime Environment (build 1.8.0_51-b16)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)

$ javac -version
javac 1.8.0_51

OS X Basics

In order to develop on OMERO, we recommend you ensure you have your Mac setup for development. The first step to achieving this is to create a .bash_profile file in the root directory of your user folder.

To create a .bash_profile from terminal, if one does not already exist:

$ touch ~/.bash_profile

To open your .bash_profile in a text editor, such as the built-in TextEdit app, use:

$ open -a TextEdit.app ~/.bash_profile

Note

If you want changes to your .bash_profile to take effect without restarting OS X, run:

$ source ~/.bash_profile

Requirements

1. Open a command-line terminal and install git if not already present:

   $ brew install git
   

2. Install PostgreSQL database server:

   $ brew install postgresql
   

   To ensure PostgreSQL uses UTF-8 encoding, open your bash profile and add the following environment variables:

   export LANG=en_US.UTF-8
   export LANGUAGE=en_US:en
   

3. OMERO depends on Ice 3.6 and unfortunately does not run with the latest version of Ice at this time (Ice 3.7.3). To obtain Ice 3.6, we need to add a tap to Homebrew:

   $ brew tap zeroc-ice/tap
   $ brew install zeroc-ice/tap/ice36
   

Note

If you already have a version of Ice that is not 3.6 installed, you can instruct Homebrew to unlink it using `$ brew unlink ice`. You can then instruct Homebrew to link to Ice 3.6 using `$ brew link ice@36`

4. Install Python provided by Homebrew:

   $ brew install python
   

   Homebrew installs Python in the following location:

   '/usr/local/opt/python/libexec/bin'
   

   Follow the instructions from the brew Python install and set your system to use the Homebrew version of Python rather than the Python shipped with OS X. Add the following line to your .bash_profile:

   export PATH="/usr/local/opt/python/libexec/bin:$PATH"
   

5. Check that Python is working and is version 2.7.x:

   $ which python
   /usr/local/opt/python/libexec/bin/python
   
   $ python --version
   Python 2.7.13
   

6. For developing with OMERO, or Python in general, we recommend the use of Virtualenv. Virtualenv allows development of Python applications without having to worry about clashing third-party packages for different Python projects.

   Use pip to get Virtualenv:

   $ pip install virtualenv
   

   With Virtualenv installed, create a virtual environment:

   $ virtualenv ~/Virtual/omero
   

   This will create a folder to hold Python libraries in the the directory ~/Virtual/omero/lib

Note

You can activate the Virtualenv environment that we created using:

$ source ~/Virtual/omero/bin/activate

This will switch to using Pip and Python in the Virtualenv directory ~/Virtual/omero/bin and any Pip libraries you install, whilst the Virtualenv is activated, will be installed to source ~/Virtual/omero/lib.

Note

(Optional) To make starting a Virtualenv environment easier, you can add an alias to your .bash_profile:

alias startVmOmero="source ~/Virtual/omero/bin/activate"

Using the command-line terminal, reload your .bash_profile:

$ source ~/.bash_profile

Now you can activate the Virtualenv environment using:

$ startVmOmero

7. Install NGINX:

   $ brew install nginx
   

OMERO installation

Pre-built server

1. Using the command-line terminal, prepare a place for your OMERO server to be downloaded to.

   Find the current OMERO.server zip from the downloads page. Download and extract the OMERO.server-x.x.x-ice36-bxx.zip.

Locally built server

1. Clone the source code from the project’s GitHub account to build locally:

   $ git clone --recursive git://github.com/openmicroscopy/openmicroscopy
   

2. Navigate terminal into the openmicroscopy that was just created by performing the previous step:

   $ cd openmicroscopy
   

3. Execute the build script (this will take a few minutes, depending on how fast your Mac is)

   $ ./build.py
   

See also

Installing OMERO from source

Developer documentation page on how to check out to source code

Build System

Developer documentation page on how to build the OMERO.server

4. Once the build completes, the OMERO server build output will be located in openmicroscopy/dist.

OMERO configuration

1. Open your .bash_profile in a text editor, such as the built-in TextEdit app:

   $ open -a TextEdit.app ~/.bash_profile
   

   Add an environment variable OMERO_SERVER to the .bash_profile which points to the location of the OMERO executable:

   # Pre-built server...
   export OMERO_SERVER=/path/to/OMERO.server-x.x.x-ice36-bxx
   # ...OR locally built server
   export OMERO_SERVER=/path/to/openmicroscopy/dist
   

   and add the OMERO executable to the OS X PATH:

   # Add the OMERO distribution to PATH
   export PATH=$OMERO_SERVER/bin:$PATH
   

   Using the command-line terminal, reload your .bash_profile using:

   $ source ~/.bash_profile
   

   To ensure OMERO is correctly linked into your OS X PATH, type the following in terminal and ensure you get a similar output:

   $ which omero
   # Pre-built server...
   /path/to/OMERO.server-x.x.x-ice36-bxx/bin/omero
   # ...OR locally built server
   /path/to/openmicroscopy/dist/bin/omero
   

3. Activate the Virtualenv environment that we created earlier in the “Requirements” section:

   $ source ~/Virtual/Omero/bin/activate
   

4. Install Python dependencies using pip:

   $ pip install -r "${OMERO_SERVER}/share/web/requirements-py27-all.txt"
   

Database

1. From a fresh command-line terminal, start the database server:

   $ pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w start
   

Note

(Optional) To make life easier, you can add an `alias` to your .bash_profile to start and stop the Postgres service:

alias startPg='pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w start'
alias stopPg='pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w stop'

Reload .bash_profile in OS X:

$ source ~/.bash_profile

2. To use OMERO, we need to first set up PostgreSQL. Open a command-line terminal and run the following commands to create a user called db_user and a database called omero_database:

   $ createuser -w -D -R -S db_user
   $ createdb -E UTF8 -O db_user omero_database
   

3. Now set the OMERO configuration:

   $ omero config set omero.db.name omero_database
   $ omero config set omero.db.user db_user
   $ omero config set omero.db.pass db_password
   

4. Create and run script to initialize the OMERO database:

   $ omero db script --password omero -f - | psql -h localhost -U db_user omero_database
   

Binary Repository

1. Create directory for OMERO to store its data:

   $ mkdir /OMERO
   $ omero config set omero.data.dir /OMERO
   

OMERO.web

Basic setup for OMERO using NGINX:

$ mv /usr/local/etc/nginx/nginx.conf /usr/local/etc/nginx/nginx.conf.orig
$ omero web config nginx-development > /usr/local/etc/nginx/nginx.conf
$ nginx -t
$ nginx

Note

The internal Django webserver can be used for evaluation and development. In this case please follow the instructions under OMERO.web installation for developers.

Startup and shutdown

If necessary start PostgreSQL database server:

$ pg_ctl -D /usr/local/var/postgres -l /usr/local/var/postgres/server.log -w start

Start OMERO:

$ omero admin start

Start OMERO.web:

$ omero web start

Now connect to your OMERO.server using OMERO.insight or OMERO.web with the following credentials:

U: root
P: omero

Stop OMERO.web:

$ omero web stop

Stop OMERO:

$ omero admin stop

Web configuration and maintenance

For more configuration options and maintenance advice for OMERO.web see OMERO.web administration.

Common issues

Example .bash_profile

Open your .bash_profile in a text editor, such as the built-in TextEdit app:

$ open -a TextEdit.app ~/.bash_profile

If you have followed this guide your .bash_profile should look similar to the following:

# UTF-8 and US language settings for Postgres
export LANG=en_US.UTF-8
export LANGUAGE=en_US:en

# OMERO Server distribution directory
export OMERO_SERVER=/path/to/OMERO.server-x.x.x-ice36-bxx

# Homebrew Python path
export BREW_PYTHON=/usr/local/opt/python/libexec/bin

# Full path
export PATH=$OMERO_SERVER/bin:BREW_PYTHON:$PATH

# Start a virtual environment for developing Python
alias startVmOmero='source ~/Virtual/omero/bin/activate'

General considerations

If you run into problems with Homebrew, you can always run:

$ brew update
$ brew doctor

Also, please check the Homebrew Bug Fixing Checklist.

Below is a non-exhaustive list of errors/warnings specific to the OMERO installation. Some if not all of them could possibly be avoided by removing any previous OMERO installation artifacts from your system.

Database

Check to make sure the database has been created and ‘UTF8’ encoding is used

$ psql -h localhost -U db_user -l

This command should give similar output to the following:

                        List of databases

   Name         | Owner   | Encoding |  Collation  |    Ctype    | Access privileges
----------------+---------+----------+-------------+-------------+-------------------
 omero_database | db_user | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
 postgres       | ome     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
 template0      | ome     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =c/ome           +
                |         |          |             |             | ome=CTc/ome
 template1      | ome     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =c/ome           +
                |         |          |             |             | ome=CTc/ome
(4 rows)

Macports/Fink

Warning: It appears you have MacPorts or Fink installed.

Follow uninstall instructions from the Macports guide.

PostgreSQL

If you encounter this error during installation of PostgreSQL:

Error: You must ``brew link ossp-uuid' before postgresql can be installed

try:

$ brew cleanup
$ brew link ossp-uuid

For recent versions of OS X (10.10 and above) some directories may be missing, preventing PostgreSQL from starting up. In that case, it should be sufficient to reinitialize a PostgreSQL database cluster as:

$ rm -rf /usr/local/var/postgres
$ initdb -E UTF8 /usr/local/var/postgres

See also

http://stackoverflow.com/questions/25970132/pg-tblspc-missing-after-installation-of-latest-version-of-os-x-yosemite-or-el

szip

If you encounter an MD5 mismatch error similar to this:

==> Installing hdf5 dependency: szip
==> Downloading http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz
Already downloaded: /Library/Caches/Homebrew/szip-2.1.tar.gz
Error: MD5 mismatch
Expected: 902f831bcefb69c6b635374424acbead
Got: 0d6a55bb7787f9ff8b9d608f23ef5be0
Archive: /Library/Caches/Homebrew/szip-2.1.tar.gz
(To retry an incomplete download, remove the file above.)

then manually remove the archived version located under /Library/Caches/Homebrew, since the maintainer may have updated the file.

numexpr (and other Python packages)

If you encounter an issue related to numexpr complaining about NumPy having too low a version number, verify that you have not previously installed any Python packages using pip. In the case where pip has been installed before Homebrew, uninstall it:

$ sudo pip uninstall pip

and then try running python_deps.sh again. That should install pip via Homebrew and put the Python packages in correct locations.