[ome-devel] OMERO setup notes

Tue Mar 26 12:01:26 GMT 2013

Hi Curtis,

first of all, thanks for the feedback. It is always nice to have people testing these installation instructions.
I tried to convert most of your comments into a documentation Pull Request: https://github.com/openmicroscopy/ome-documentation/pull/301
Please have a look at it and let me know if I missed important points.

Re Homebrew, note we have run into problems because Homebrew wasn't installed in the default /usr/local.

Re source installation vs downloaded tarball, I see your point and I think there are two solutions:
- either host source installation pages in the developer documentation
- or keep all installation pages under sysadmin and split section containing source code/downloads specificities
I don't have a strong opinion on which of these options is the best. As long as we can improve the visibility/navigation without increasing the developers maintenance burden, I am open to any suggestion.

Regards,
Sebastien

On 25 Mar 2013, at 20:42, Curtis Rueden wrote:

Hi again,

> Seems like the web client is receiving 404s for many static resources

After some assistance from the OMERO team, the fix was:

$ omero config set omero.web.debug True

I somehow missed this line from the OS X Homebrew walkthrough.

If a more general-purpose "Development server" section is created (and/or copied into the Linux walkthrough), this is indeed another important point.

Regards,
Curtis

On Mon, Mar 25, 2013 at 3:31 PM, Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>> wrote:
Hi all,

Looks like I spoke too soon about everything being fine with my OMERO Linux dev install. Seems like the web client is receiving 404s for many static resources [1]. Any ideas?

Thanks,
Curtis

[1] http://curtis.imagej.net/omero-web-404s.png

On Mon, Mar 25, 2013 at 3:11 PM, Curtis Rueden <ctrueden at wisc.edu<mailto:ctrueden at wisc.edu>> wrote:
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<http://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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Dr Sébastien Besson
Open Microscopy Environment / Harvard Medical School
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096
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