[ome-devel] OMERO setup notes
Curtis Rueden
ctrueden at wisc.edu
Mon Mar 25 20:42:22 GMT 2013
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> 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> 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 1) Version numbers are out of date for Ubuntu 12.04, of course.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
>>
>> ********************************************************************************
>>
>> 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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