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:

• HDF5
• NumPy points to downloads at http://sourceforge.net/projects/numpy/
• PyTables (Some packages include HDF5)

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
unknown GNU/Linux
$ gcc --version
gcc-4.8.real (Debian 4.8.1-9) 4.8.1
Copyright (C) 2013 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/hdf5-1.8.11.tar.gz"
$ tar xzf hdf5-1.8.11.tar.gz
$ cd hdf5-1.8.11
$ ./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:

% python
Python 2.7.5+ (default, Aug  4 2013, 10:07:17)
[GCC 4.8.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.test()
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version:  2.4.0
HDF5 version:      1.8.11
NumPy version:     1.7.1
Numexpr version:   2.0.1 (not using Intel's VML/MKL)
Zlib version:      1.2.8 (in Python interpreter)
LZO version:       2.06 (Aug 12 2011)
BZIP2 version:     1.0.6 (6-Sept-2010)
Blosc version:     1.1.3 (2010-11-16)
Python version:    2.7.5+ (default, Aug  4 2013, 10:07:17)
[GCC 4.8.1]
Platform:          linux2-x86_64
Byte-ordering:     little
Detected cores:    8
…

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:

• PIL: http://effbot.org/media/downloads/PIL-1.1.7.win32-py2.6.exe
• SciPy: http://sourceforge.net/projects/scipy/files/scipy/0.11.0/scipy-0.11.0-win32-superpack-python2.6.exe/download
• NumPy: http://sourceforge.net/projects/numpy/files/NumPy/1.6.2/numpy-1.6.2-win32-superpack-python2.6.exe/download
• PyTables: http://www.lfd.uci.edu/~gohlke/pythonlibs/#pytables
• HDF (with szip and zlib): http://www.hdfgroup.org/ftp/HDF5/current/bin/windows/

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)