[ome-devel] OMERO setup notes
Curtis Rueden
ctrueden at wisc.edu
Mon Mar 25 20:31:37 GMT 2013
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 1) Version numbers are out of date for Ubuntu 12.04, of course.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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