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

Java may be installed using OpenJDK from AdoptOpenJDK. See Version requirements for supported versions.

After installing JDK, check your installation works by running:

$ java --version
openjdk 11.0.5 2019-10-15
OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.5+10)
OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.5+10, mixed mode)

$ javac -version
javac 11.0.5

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. Install NGINX:

   $ brew install nginx
   

4. OMERO depends on Ice 3.6 and unfortunately does not run with the Ice version 3.7 or higher. 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`

Python

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.

We will create 2 virtual environments below, ome for omero-py and another for omero-web (which also includes omero-py). This allows more flexibility, but you can use just the omero-web virtual environment for everything if you wish.

You can create virtual environments using either conda (preferred) OR venv.

Using conda (preferred)

1. Install Conda. See miniconda for more details.

2. Create virtual environments named omeropy and omeroweb:

   $ conda create -n omeropy -c ome python=3.6 zeroc-ice36-python omero-py
   $ conda create -n omeroweb -c ome python=3.6 zeroc-ice36-python omero-web
   

3. Activate the virtual environments:

   $ conda activate omeropy
   
   # In a different terminal:
   $ conda activate omeroweb
   

4. You can now use the omero command. You will also need to ensure you are in the appropriate environment when you install additional modules:

   $ omero -h
   
   # Additional modules. For example:
   $ pip install omero-metadata
   

   Now go to the OMERO installation section below.

OR using venv

1. install Python provided by Homebrew:

   $ brew install python
   

   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. Typically:

   $ brew link python
   

2. Check that Python is working and is version 3.7.x:

   $ which python3
   /usr/local/bin/python3
   
   $ python3 --version
   Python 3.7.4
   

3. Create a virtual environments for omero-py and/or omero-web using Python 3:

   $ python3 -mvenv ~/Virtual/omeropy
   $ python3 -mvenv ~/Virtual/omeroweb
   

4. Activate the Virtualenv environment(s) and install modules:

   $ source ~/Virtual/omeropy/bin/activate
   $ pip install "omero-py>=\ |version_py|"
   
   # In a different terminal:
   $ source ~/Virtual/omeroweb/bin/activate
   $ pip install "omero-web>=\ |version_web|"
   

5. You can now use the omero command in either virtual environment. You will also need to ensure you are in the appropriate environment when you install additional modules:

   $ omero -h
   
   # Additional modules. For example:
   $ pip install omero-metadata
   

OMERO installation

Pre-built server

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

2. Find the current OMERO.server zip from the downloads page.

3. 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/ome/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
   

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

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

OMERO configuration

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

   $ open -a TextEdit.app ~/.bash_profile
   

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

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

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

   $ source ~/.bash_profile
   

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
   

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. Activate the omeropy env:

   $ conda activate omeropy
   # OR
   $ source ~/Virtual/omeropy/bin/activate
   

4. 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
   

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

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

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 :file:`.bash_profile` in OS X::

$ source ~/.bash_profile

Binary Repository

1. Create directory for OMERO to store its data:

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

OMERO.web

1. Activate the omeroweb env:

   $ conda activate omeroweb
   # OR
   $ source ~/Virtual/omeroweb/bin/activate
   

2. 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

Activate the omeropy env and start OMERO:

$ conda activate omeropy
# OR
$ source ~/Virtual/omeropy/bin/activate

$ omero admin start

Activate the omeroweb env and start OMERO.web:

$ conda activate omeroweb
# OR
$ source ~/Virtual/omeroweb/bin/activate
$ omero web start

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

U: root
P: omero

Activate the omeroweb env as above, and stop OMERO.web:

$ omero web stop

Activate the omeropy env as above and stop OMERO:

$ omero admin stop

Web configuration and maintenance

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

Common issues

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)

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

https://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.