[ome-devel] OMERO setup notes
Curtis Rueden
ctrueden at wisc.edu
Tue Mar 26 15:25:49 GMT 2013
Hi Sebastian,
> 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.
Thanks for the rapid turnaround! I like the changes. I wrote a few thoughts
in the PR.
> - or keep all installation pages under sysadmin and split section
> containing source code/downloads specificities
Since this option is what the PR does at the moment, and is less
disruptive, I think it's fine.
> I don't have a strong opinion on which of these options is the best.
Me either.
> As long as we can improve the visibility/navigation without increasing
> the developers maintenance burden, I am open to any suggestion.
Right. It might we worth adding a blurb to the top of the two sysadmin
walkthrough pages which explicitly states something like:
This walkthrough covers installation of OMERO from either a binary
distribution or from source. Both installations are very similar—the
prerequisites must be installed in either case—with differences outlined
below in the "Development server" section.
Lastly, we could add a new bullet point to the toplevel OMERO developer
documentation page, in the "Introduction to OMERO" section: "Installing
OMERO from source" with two sub-items, "OS X" and "Linux", which link to
the two respective walkthroughs. Such a link would have helped me a lot
personally, because the first thing I looked for was an "installing OMERO
from source" sort of page in the developer documentation section. And while
that page does state at the top that "Instructions on downloading,
installation and administering OMERO can be found under the System
Administrator Documentation of the main site", this sentence implies (to
me) that those pages will be about downloading and installing from tarball
only, not from source.
Regards,
Curtis
On Tue, Mar 26, 2013 at 7:01 AM, Sebastien Besson <s.besson at dundee.ac.uk>wrote:
> 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> 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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> ome-devel at lists.openmicroscopy.org.uk
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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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