[ome-devel] OMERO setup notes

Mon Mar 25 20:11:24 GMT 2013

Hi everyone,

I recently set up an OMERO developer installation (i.e.., from
openmicroscopy.git), and thought I would pass along some notes, comments
and suggestions relating to my experiences. Perhaps it is useful to help
refine the documentation.

First I tried setting up OMERO on an OS X workstation using Homebrew by
following the walkthrough guide [1]. Unfortunately, I ran into quite a bit
of trouble [3].

Ultimately, I gave up and decided to install into an Ubuntu Linux VM
instead according to the Linux walkthrough guide [2], which I now have
working [4]. The directions in the Linux walkthrough worked. Some brief
comments there:

1) Version numbers are out of date for Ubuntu 12.04, of course.

2) python-tables installed OK (I think), so I skipped the liblzo2-2 install.

3) I used openjdk-7-jdk instead of building a sun-java6-jdk as shown in the
instructions, and OMERO seems to run fine (so far).

Note that the OS X Homebrew guide has a small "Developer server" section,
but the corresponding Linux walkthrough guide has no such section.

In general, I did not know which guide to follow for a developer
installation from source, rather than one from a downloaded tarball. Would
it make sense to have a separate, dedicated page for that, which links to
the other guides as appropriate (for prereqs etc.) but which also explains
the differences when building and running from source?

Regards,
Curtis

[1]
https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html

[2]
https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-linux.html

[3] Selected logs from OS X Homebrew installation attempt:

$ sw_vers
ProductName: Mac OS X
ProductVersion: 10.6.8
BuildVersion: 10K549

$ brew --config
HOMEBREW_VERSION: 0.9.4
ORIGIN: https://github.com/mxcl/homebrew.git
HEAD: 35633640f3f322667ac067c73ab0b4c84022710c
HOMEBREW_PREFIX: /Users/curtis/brew
HOMEBREW_CELLAR: /Users/curtis/brew/Cellar
CPU: dual-core 64-bit penryn
OS X: 10.6.8-i386
Xcode: 3.2.6
GCC-4.0: build 5494
GCC-4.2: build 5666
LLVM-GCC: build 2335
Clang: 1.7 build 77
X11: 2.3.6 => /usr/X11
System Ruby: 1.8.7-358
Perl: /usr/bin/perl
Python: /Users/curtis/brew/bin/python =>
/Users/curtis/brew/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby =>
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby

$ brew install postgresql
==> Downloading
http://ftp.postgresql.org/pub/source/v9.2.3/postgresql-9.2.3.tar
########################################################################
100.0%
==> Patching
patching file src/pl/plpython/Makefile
patching file contrib/uuid-ossp/uuid-ossp.c
Warning: Detected a framework Python that does not have 64-bit support in:
/Library/Frameworks/Python.framework/Versions/Current/Python

e configure script seems to prefer this version of Python over any others,
 you may experience linker problems as described in:
http://osdir.com/ml/pgsql-general/2009-09/msg00160.html

 fix this issue, you may need to either delete the version of Python
own above, or move it out of the way before brewing PostgreSQL.

te that a framework Python in /Library/Frameworks/Python.framework is
e "MacPython" version, and not the system-provided version which is in:
/System/Library/Frameworks/Python.framework
==> ./configure --prefix=/Users/curtis/brew/Cellar/postgresql/9.2.3
--datadir=/U
==> make install-world
/bin/sh ../../config/install-sh -c -d
'/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension'
/bin/sh ../../config/install-sh -c -m 755  adminpack.so
'/Users/curtis/brew/Cellar/postgresql/9.2.3/lib/adminpack.so'
/bin/sh ../../config/install-sh -c -m 644 ./adminpack.control
'/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'
/bin/sh ../../config/install-sh -c -m 644 ./adminpack--1.0.sql
 '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'
make: *** [install-world-contrib-recurse] Error 2

$ sudo mv /Library/Frameworks/Python.framework /Library/Frameworks/pfx

$ brew install postgresql
==> Downloading
http://ftp.postgresql.org/pub/source/v9.2.3/postgresql-9.2.3.tar
Already downloaded:
/Users/curtis/Library/Caches/Homebrew/postgresql-9.2.3.tar.bz2
==> Patching
patching file src/pl/plpython/Makefile
patching file contrib/uuid-ossp/uuid-ossp.c
==> ./configure --prefix=/Users/curtis/brew/Cellar/postgresql/9.2.3
--datadir=/U
==> make install-world
/bin/sh ../../config/install-sh -c -m 755  adminpack.so
'/Users/curtis/brew/Cellar/postgresql/9.2.3/lib/adminpack.so'
/bin/sh ../../config/install-sh -c -d
'/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension'
/bin/sh ../../config/install-sh -c -m 644 ./adminpack.control
'/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'
/bin/sh ../../config/install-sh -c -m 644 ./adminpack--1.0.sql
 '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'
make: *** [install-world-contrib-recurse] Error 2

$ sudo mv /Library/Frameworks/pfx /Library/Frameworks/Python.framework

$ brew doctor
Warning: Your Homebrew is not installed to /usr/local
You can install Homebrew anywhere you want, but some brews may only build
correctly if you install in /usr/local. Sorry!

(Note: the logs above do not include another failure I had when installing
berkeley-db46.)

[4] Selected logs from OMERO Linux installation:

$ omero config get omero.db.name
********************************************************************************

        ERROR: Could not import omero.cli! (No module named omero.cli)

        This means that your installation is incomplete. Contact
        the OME mailing lists for more information:

        http://www.openmicroscopy.org/site/community

        If you are building from source, please supply the build log
        as well as which version you are building from. If you
        downloaded a distribution, please provide which link you
        used.

********************************************************************************

        Debugging Info:
        --------------
        CWD=/home/curtis/code/ome/openmicroscopy
        VERSION=2.7.3 (default, Aug  1 2012, 05:14:39)  [GCC 4.6.3]
        OMERO_HOME=/home/curtis/code/ome/openmicroscopy
        PYTHONPATH=['/home/curtis/code/ome/openmicroscopy/lib/python',
'/home/curtis/code/ome/openmicroscopy/var/lib',
'/home/curtis/code/ome/openmicroscopy/dist/bin',
'/usr/lib/pymodules/python2.7', '/home/curtis/code/ome/openmicroscopy',
'/usr/lib/python2.7', '/usr/lib/python2.7/plat-linux2',
'/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old',
'/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages',
'/usr/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PIL',
'/usr/lib/python2.7/dist-packages/gst-0.10',
'/usr/lib/python2.7/dist-packages/gtk-2.0',
'/usr/lib/python2.7/dist-packages/ubuntu-sso-client',
'/usr/lib/python2.7/dist-packages/ubuntuone-client',
'/usr/lib/python2.7/dist-packages/ubuntuone-control-panel',
'/usr/lib/python2.7/dist-packages/ubuntuone-couch',
'/usr/lib/python2.7/dist-packages/ubuntuone-installer',
'/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol',
'/home/curtis/code/ome/openmicroscopy/lib/fallback']

To fix, I needed to set OMERO_HOME to "openmicroscopy/dist" subfolder, so
it could find the Python libs in lib.

It would be good to add this as a note to both of the walkthrough guides,
in the "Developer server" section.
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