Overview
This walk-through demonstrates how to install OMERO on a clean Mac OS X 10.7 Lion system 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.
The instructions provided here depend on Homebrew 0.9 or later, including support for the brew tap command. These instructions are implemented in a series of automated scripts which install OMERO via Homebrew from a fresh configuration.
Install the OS X Developer Tools. This procedure is regularly tested with the following configuration:
| Model Identifier | Mac OS X version | Xcode version |
|---|---|---|
| MacBookPro8,2 (Intel Core i7, 2.3 GHz, 8 GB RAM) | 10.7.5 | 4.6 |
Note
For Xcode 4.x, make sure that the Command line tools are installed (Preferences ‣ Downloads ‣ Components)
You need Java which comes as standard on OS X.
$ java -version
java version "1.6.0_33"
Java(TM) SE Runtime Environment (build 1.6.0_33-b03-424-11M3720)
Java HotSpot(TM) 64-Bit Server VM (build 20.8-b03-424, mixed mode)
Follow the installation instructions on the Homebrew wiki. All requirements for OMERO will be installed to /usr/local.
$ ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go/install)"
$ brew install git
If you are having issues with curl, see the curl (Mac 10.5 only) section under Common issues.
The installation of OMERO via Homebrew depends on two alternate repositories containing extra formulas: https://github.com/Homebrew/homebrew-science for the HDF5 formula and https://github.com/ome/homebrew-alt for all the OME-provided formulas and older versions of Ice.
You can install OMERO using either the system-wide Python or the Python provided by Homebrew. For a more thorough description of the latter solution, look at the Homebrew and Python page. Note that the automated script linked above tests the OMERO installation using the Homebrew Python.
If using system-wide Python, check it is installed and its version.
$ python --version
Python 2.7.3
To install the Python provided by Homebrew:
$ brew install python
Independently of the chosen Python, you can setup and use virtual environments to install the OMERO Python dependencies (see Python dependencies).
Note
The Homebrew formulas 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.
If you just want a deployment of the 5.0.8 release of OMERO.server then a simple Homebrew install is sufficient, e.g.
$ brew tap homebrew/science
$ brew tap ome/alt
$ brew install omero
This should install OMERO along with most of the non-Python requirements.
The default version of Ice installed by the OMERO formula is Ice 3.5. To install OMERO with Ice 3.4, use:
$ brew install omero --with-ice34
or to install OMERO with Ice 3.3, use:
$ brew install omero --with-ice33
Additional installation options can be listed using the info command:
$ brew info omero
If you wish to pull OMERO.server from the git repo for development purposes then it is worth setting up OMERO.server manually. First use Homebrew to install the OMERO dependencies:
$ brew tap homebrew/science
$ brew tap ome/alt
$ brew install --only-dependencies omero
The default version of Ice installed by the OMERO formula is Ice 3.5. To install the OMERO dependencies with Ice 3.4, use:
$ brew install --only-dependencies omero --with-ice34
or to install the OMERO dependencies with Ice 3.3, use:
$ brew install --only-dependencies omero --with-ice33
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 if you do not have another PostgreSQL installation that you can use.
$ postgres --version # Check if you have postgres
postgres (PostgreSQL) 9.3.4
$ brew install postgresql
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:
$ cd /usr/local
$ bash bin/omero_python_deps
If you use a development server, execute the python_deps.sh script under docs/install:
$ cd ~/code/projects/OMERO
$ bash docs/install/python_deps.sh
If you encounter problems with the installation script, please take a look at Common issues.
Edit your .profile as appropriate. The following are indicators of required entries and correspond to a Homebrew installation of OMERO 5.0.8:
export PYTHONPATH=$(brew --prefix omero)/lib/python
export PATH=/usr/local/bin:/usr/local/sbin:/usr/local/lib/node_modules:$PATH
If you have installed Ice 3.3 or Ice 3.4, you will need to specify the path to Ice Python and dynamic libraries:
export PYTHONPATH=$(brew --prefix omero)/lib/python:$ICE_HOME/python
export DYLD_LIBRARY_PATH=$ICE_HOME/lib:$DYLD_LIBRARY_PATH
where ICE_HOME needs to be replaced by $(brew --prefix zeroc-ice33) or $(brew --prefix zeroc-ice34) depending on your configuration.
Note
If you have a local .bash_profile file, it will override your .profile configuration file.
Note
On Mac OS X Lion, a version of PostgreSQL is already installed. If you get an error like the following:
psql: could not connect to server: Permission denied
Is the server running locally and accepting
connections on Unix domain socket "/var/pgsql_socket/.s.PGSQL.5432"?
make sure /usr/local/bin is at the beginning of your PATH (see also this post).
Start the PostgreSQL server.
$ initdb /usr/local/var/postgres
$ brew services start postgresql
$ pg_ctl -D /usr/local/var/postgres/ -l /usr/local/var/postgres/server.log start
Create a user, a database and add the PL/pgSQL language to your database.
$ createuser -P -D -R -S db_user
Enter password for new role: # db_password
Enter it again: # db_password
$ createdb -O db_user omero_database
$ createlang plpgsql omero_database
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 tell OMERO.server about our 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 $ omero db script Please enter omero.db.version [OMERO5.0]: Please enter omero.db.patch [0]: Please enter password for new OMERO root user: # root_password Please re-enter password for new OMERO root user: # root_password Saving to ~/OMERO5.0__0.sql
Then enter the name of the .sql (see last line above) in the next command, to create the database:
$ psql -h localhost -U db_user omero_database < OMERO5.0__0.sql
Now create a location to store OMERO data, e.g.
$ mkdir -p ~/var/OMERO.data
and tell OMERO.server this location:
$ omero config set omero.data.dir ~/var/OMERO.data
We can inspect the OMERO.server configuration settings using:
$ omero config get
Now 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.
curl: (60) SSL certificate problem, verify that the CA cert is OK. Details:
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed
Use export GIT_SSL_NO_VERIFY=1 before running failing brew commands.
Warning: It appears you have MacPorts or Fink installed.
Follow uninstall instructions from the Macports guide.
==> Installing postgresql dependency: readline
Error: No such file or directory - /usr/bin/cc
For Xcode 4.3.2 make sure Xcode Command Line Tools are installed (see comment).
Error: You must ``brew link ossp-uuid' before postgresql can be installed
Try:
$ brew cleanup
$ brew link ossp-uuid
Error: Failed executing: cd cpp && make M PP_HOME=/Users/sebastien/apps/ OMERO.libs/Cellar/mcpp/2.7.2 DB_HOME=/Users/sebastien/apps/OMERO.libs/Cellar/berkeley- db46/4.6.21 OPTIMIZE=yes prefix=/Users/sebastien/apps/OMERO.libs/Cellar/zeroc-ice33/3.3 embedded_runpath_prefix=/Users/sebastien/apps/OMERO.libs/Cellar/zeroc-ice33/3.3 install
We have had problems building zeroc-ice33 under MacOS 10.7.3 and 10.6.8 (see #8075). You can try installing zeroc-ice34 (Ice 3.4) instead. If you decide to go with zeroc-ice33, make sure that you do not have DYLD_LIBRARY_PATH set to an existing Ice’s installation lib directory path. In essence your .bash_profile shouldn’t have any OMERO-related environment variables set before executing the installation script.
==> 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.)
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 a too low version number, verify that you have not before installed any Python packages using pip. In the case where pip has been installed before homebrew, uninstall it:
$ sudo pip uninstall pip
After that try running python_deps.sh again. That should install pip via Homebrew and put the Python packages in correct folders.
gfortran currently fails to build on 32-bit 10.6.8 machines (see https://github.com/mxcl/homebrew/issues/17776)