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This documentation is for OMERO 4.4 and is no longer being updated, to see the documentation for the latest release, refer to http://openmicroscopy.org/site/support/omero/

Installing OMERO.tables

OMERO.tables provide a way to efficiently store large, tabular results within OMERO. If you would like to find out more about the use of the OMERO.tables API, see OMERO.analysis

Requirements

If you would like to help test the Tables API, you will need the following installed:

Unix

PyTables is likely available from the package repository of your Unix-flavor. This includes Mac OS X (homebrew), Debian and Ubuntu (apt-get), Centos (yum), and SuSE (yast). Here we’ve shown manual instructions using virtualenv.

Manually

$ virtualenv $HOME/virtualenv
$ uname -o -p
i686 GNU/Linux
$ gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-44)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.3.tar.gz
$ tar xzf hdf5-1.8.3.tar.gz
$ cd hdf5-1.8.3
$ ./configure --prefix=$HOME/virtualenv
$ make
$ make install
$ export LD_LIBRARY_PATH=$HOME/virtualenv/lib
$ . $HOME/virtualenv/bin/activate
$ easy_install tables

Checking that it works

After that, the following should succeed:

josh@mac:~$ python
Python 2.5.4 (r254:67916, Jun 24 2009, 20:23:29)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:  2.1
HDF5 version:      1.8.3
NumPy version:     1.3.0
Zlib version:      1.2.3
BZIP2 version:     1.0.5 (10-Dec-2007)
Python version:    2.5.4 (r254:67916, Jun 24 2009, 20:23:29)
[GCC 4.0.1 (Apple Computer, Inc. build 5370)]
Platform:          darwin-i386
Byte-ordering:     little
…

Once the required Python libraries are installed, starting OMERO will automatically start up the OMERO.tables service; there should be no need for further configuration or interaction.

Windows

The following specific packages have been tested on Windows 7 Enterprise:

After installing all the Windows prerequisites OMERO.tables should start up during the OMERO.server startup. It can be verified by looking at the output of omero admin diagnostics:

Server:     Tables-0                       active (pid = 3176, enabled)