Overview
This walk-through demonstrates how to install OMERO on a clean Mac OS X system (10.8 or later) using Homebrew. Note that this demonstrates how to install OMERO.server from the source code via Homebrew, in addition to all its prerequisites. The default instructions for UNIX platforms in the OMERO.server installation guide are all you need to install the prerequisites with Homebrew and then install the server zip from the downloads page or build from source.
These instructions are implemented in a series of automated scripts which install OMERO via Homebrew from a fresh configuration.
Homebrew requires the latest version of Xcode.
Install Xcode from the App Store; if you have already installed it, make sure all the latest updates are installed
Run the following command to install the command-line tools for Xcode:
xcode-select --install
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_31"
Java(TM) SE Runtime Environment (build 1.8.0_31-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)
$ javac -version
javac 1.8.0_31
Follow the installation instructions on the Homebrew wiki. All the requirements for OMERO will be installed under /usr/local.
$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
$ brew install git
The installation of OMERO via Homebrew depends upon two alternate repositories containing extra formulae: https://github.com/Homebrew/homebrew-science for the HDF5 formula and https://github.com/ome/homebrew-alt for all the OME-provided formulae and older versions of Ice. To add these, run:
$ brew tap homebrew/science
$ brew tap ome/alt
Lastly, make sure /usr/local/bin is before /usr/bin in your PATH. For example, add the following to ~/.profile and then start a new shell for the change to take effect:
export PATH=/usr/local/bin:/usr/local/sbin:$PATH
You can install OMERO using either the Python 2.7 provided by Homebrew, or the system-wide Python 2.7 provided by MacOS X. Homebrew Python is recommended since it makes using Homebrew-provided modules simpler, for example the Ice python bindings needed by OMERO. For a more thorough description of the Homebrew solution, see the Homebrew and Python page. Note that the automated script linked above tests the OMERO installation using the Homebrew Python.
To install the Python provided by Homebrew:
$ brew install python
Check that Python is working and is version 2.7:
$ /usr/local/bin/python --version
Python 2.7.9
If using system Python, add the following to ~/.profile and then start a new shell for the change to take effect:
export PYTHONPATH=$(brew --prefix omero)/lib/python
If using Homebrew Python, this will be on the default module path.
Note
If you have a local .bash_profile file, it will override your .profile configuration file.
Independently of the chosen Python, you can set up and use virtual environments to install the OMERO Python dependencies (see Python dependencies).
Note
The Homebrew formulae used below provide Python bindings. As described in Homebrew and Python, you should not be in an active virtual environment when you brew install them.
To install and deploy the 5.1.4 release of OMERO.server, run:
$ brew install omero
This should install OMERO along with most of the non-Python requirements.
Additional installation options can be listed using the info command:
$ brew info omero
The default version of Ice installed by the OMERO formula is currently Ice 3.5.
If you wish to build OMERO.server from source for development purposes, using the git repository, first use Homebrew to install the OMERO dependencies:
$ brew install --only-dependencies omero
The default version of Ice installed by the OMERO formula is currently Ice 3.5.
Prepare a place for your OMERO code to live, e.g.
$ mkdir -p ~/code/projects/OMERO
$ cd ~/code/projects/OMERO
If you installed Ice 3.5, you will need to set SLICEPATH to be able to build the server, i.e. export SLICEPATH=/usr/local/share/Ice-3.5/slice.
If you want the development version of OMERO.server, you can clone the source code from the project’s GitHub account to build locally:
$ git clone --recursive git://github.com/openmicroscopy/openmicroscopy
$ cd openmicroscopy && ./build.py
Note
If you have a GitHub account and you plan to develop code for OMERO, you should make a fork into your own account and then clone this fork to your local development machine, e.g.
$ git clone --recursive git://github.com/YOURNAMEHERE/openmicroscopy
$ cd openmicroscopy && ./build.py
See also
Install PostgreSQL:
$ brew install postgresql
$ postgres --version
postgres (PostgreSQL) 9.4.1
The Python dependencies can be installed in the system-wide Python site-packages, in the Homebrew Python site-packages or within a virtual environment. If you are using the system-wide Python site-packages, you may need to use sudo to install the dependencies. If you are using a virtual environment, activate it before calling the Python dependencies installation script.
If you installed OMERO using Homebrew, execute the omero_python_deps script:
$ omero_python_deps
If you use a development server, execute the python_deps.sh script under docs/install:
$ cd ~/code/projects/OMERO
$ docs/install/python_deps.sh
If you encounter problems with the installation script, please take a look at Common issues.
Create a new database cluster:
$ initdb -E UTF8 /usr/local/var/postgres
Start the PostgreSQL server.
If you wish to use brew services to start postgresql, you will first need to install it, then start the service:
$ brew tap gapple/services
$ brew services start postgresql
Alternatively, to start by hand:
$ pg_ctl -D /usr/local/var/postgres/ -l /usr/local/var/postgres/server.log start
It is also possible to configure launchd to start PostgreSQL at boot
Create a user and database:
$ createuser -P -D -R -S db_user
Enter password for new role: # enter db_password
Enter it again: # enter db_password
$ createdb -E UTF8 -O db_user omero_database
Note db_user and db_password should be replaced with a username and password of your choice. Record these for future use.
Check to make sure the database has been created.
$ 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)
Now configure OMERO.server to connect to the newly-created database:
$ omero config set omero.db.name omero_database
$ omero config set omero.db.user db_user
$ omero config set omero.db.pass db_password
And then, generate the database schema:
$ omero db script --password secretpassword
You should see output similar to this:
Using OMERO5.1 for version
Using 1 for patch
Using password from commandline
Saving to /home/omero/OMERO5.1__1.sql
Then run the SQL commands in the generated schema file to create the database:
$ psql -h localhost -U db_user omero_database < OMERO5.1__1.sql
Now create a location to store OMERO data, for example:
$ mkdir -p ~/var/OMERO.data
and configure OMERO.server to use this location:
$ omero config set omero.data.dir ~/var/OMERO.data
The OMERO.server configuration settings can be inspected using:
$ omero config get
Next, start the OMERO.server:
$ omero admin start
Now connect to your OMERO.server using OMERO.insight with the following credentials:
U: root
P: root_password
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.
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.
Warning: It appears you have MacPorts or Fink installed.
Follow uninstall instructions from the Macports guide.
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
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.
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.