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<div>Hi Curtis,</div>
<div><br>
</div>
<div>first of all, thanks for the feedback. It is always nice to have people testing these installation instructions. </div>
<div>I tried to convert most of your comments into a documentation Pull Request: <a href="https://github.com/openmicroscopy/ome-documentation/pull/301">https://github.com/openmicroscopy/ome-documentation/pull/301</a></div>
<div>
<div>Please have a look at it and let me know if I missed important points.</div>
<div><br>
</div>
<div>Re Homebrew, note we have run into problems because Homebrew wasn't installed in the default /usr/local.</div>
<div><br>
</div>
<div>Re source installation vs downloaded tarball, I see your point and I think there are two solutions: </div>
<div>- either host source installation pages in the developer documentation </div>
<div>- or keep all installation pages under sysadmin and split section containing source code/downloads specificities</div>
<div>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.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Sebastien</div>
<div><br>
</div>
<div>On 25 Mar 2013, at 20:42, Curtis Rueden wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Hi again,
<div><br>
</div>
<div>
<div>> Seems like the web client is receiving 404s for many static resources</div>
</div>
<div><br>
</div>
<div style="">After some assistance from the OMERO team, the fix was:</div>
<div style=""><br>
</div>
<div style="">
<div>$ omero config set omero.web.debug True</div>
<div><br>
</div>
<div style="">I somehow missed this line from the OS X Homebrew walkthrough.</div>
<div style=""><br>
</div>
<div style="">If a more general-purpose "Development server" section is created (and/or copied into the Linux walkthrough), this is indeed another important point.</div>
<div style=""><br>
</div>
<div style="">Regards,</div>
<div style="">Curtis</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Mar 25, 2013 at 3:31 PM, Curtis Rueden <span dir="ltr">
<<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
<div dir="ltr">Hi all,
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Curtis</div>
<div><br>
</div>
<div>[1] <a href="http://curtis.imagej.net/omero-web-404s.png" target="_blank">http://curtis.imagej.net/omero-web-404s.png</a></div>
</div>
<div class="">
<div class="h5">
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, Mar 25, 2013 at 3:11 PM, Curtis Rueden <span dir="ltr">
<<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left-width:1px; border-left-color:rgb(204,204,204); border-left-style:solid; padding-left:1ex">
<div dir="ltr">Hi everyone,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>
<div>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].</div>
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>1) Version numbers are out of date for Ubuntu 12.04, of course.</div>
<div><br>
</div>
<div>2) python-tables installed OK (I think), so I skipped the liblzo2-2 install.</div>
<div><br>
</div>
<div>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).</div>
<div>
<div><br>
</div>
<div>Note that the OS X Homebrew guide has a small "Developer server" section, but the corresponding Linux walkthrough guide has no such section.</div>
<div><br>
</div>
<div>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?</div>
</div>
<div><br>
</div>
</div>
<div>
<div>Regards,<br>
</div>
</div>
<div>Curtis</div>
<div><br>
</div>
<div>[1] <a href="https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html" target="_blank">
https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-homebrew.html</a></div>
<div><br>
</div>
<div>[2] <a href="https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-linux.html" target="_blank">
https://www.openmicroscopy.org/site/support/omero4/sysadmins/unix/server-install-linux.html</a></div>
<div><br>
</div>
<div>[3] Selected logs from OS X Homebrew installation attempt:</div>
<div><br>
</div>
<div>$ sw_vers</div>
<div>ProductName:<span style="white-space:pre-wrap"> </span>Mac OS X</div>
<div>ProductVersion:<span style="white-space:pre-wrap"> </span>10.6.8</div>
<div>BuildVersion:<span style="white-space:pre-wrap"> </span>10K549</div>
<div><br>
</div>
<div>$ brew --config</div>
<div>HOMEBREW_VERSION: 0.9.4</div>
<div>ORIGIN: <a href="https://github.com/mxcl/homebrew.git" target="_blank">https://github.com/mxcl/homebrew.git</a></div>
<div>HEAD: 35633640f3f322667ac067c73ab0b4c84022710c</div>
<div>HOMEBREW_PREFIX: /Users/curtis/brew</div>
<div>HOMEBREW_CELLAR: /Users/curtis/brew/Cellar</div>
<div>CPU: dual-core 64-bit penryn</div>
<div>OS X: 10.6.8-i386</div>
<div>Xcode: 3.2.6</div>
<div>GCC-4.0: build 5494</div>
<div>GCC-4.2: build 5666</div>
<div>LLVM-GCC: build 2335</div>
<div>Clang: 1.7 build 77</div>
<div>X11: 2.3.6 => /usr/X11</div>
<div>System Ruby: 1.8.7-358</div>
<div>Perl: /usr/bin/perl</div>
<div>Python: /Users/curtis/brew/bin/python => /Users/curtis/brew/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/bin/python2.7</div>
<div>Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby</div>
<div><br>
</div>
<div>$ brew install postgresql</div>
<div>==> Downloading <a href="http://ftp.postgresql.org/pub/source/v9.2.3/postgresql-9.2.3.tar" target="_blank">
http://ftp.postgresql.org/pub/source/v9.2.3/postgresql-9.2.3.tar</a></div>
<div>######################################################################## 100.0%</div>
<div>==> Patching</div>
<div>patching file src/pl/plpython/Makefile</div>
<div>patching file contrib/uuid-ossp/uuid-ossp.c</div>
<div>Warning: Detected a framework Python that does not have 64-bit support in:</div>
<div>/Library/Frameworks/Python.framework/Versions/Current/Python</div>
<div><br>
</div>
<div>e configure script seems to prefer this version of Python over any others,</div>
<div> you may experience linker problems as described in:</div>
<div><a href="http://osdir.com/ml/pgsql-general/2009-09/msg00160.html" target="_blank">http://osdir.com/ml/pgsql-general/2009-09/msg00160.html</a></div>
<div><br>
</div>
<div> fix this issue, you may need to either delete the version of Python</div>
<div>own above, or move it out of the way before brewing PostgreSQL.</div>
<div><br>
</div>
<div>te that a framework Python in /Library/Frameworks/Python.framework is</div>
<div>e "MacPython" version, and not the system-provided version which is in:</div>
<div>/System/Library/Frameworks/Python.framework</div>
<div>==> ./configure --prefix=/Users/curtis/brew/Cellar/postgresql/9.2.3 --datadir=/U</div>
<div>==> make install-world</div>
<div>/bin/sh ../../config/install-sh -c -d '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension'</div>
<div>/bin/sh ../../config/install-sh -c -m 755 adminpack.so '/Users/curtis/brew/Cellar/postgresql/9.2.3/lib/adminpack.so'</div>
<div>/bin/sh ../../config/install-sh -c -m 644 ./adminpack.control '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'</div>
<div>/bin/sh ../../config/install-sh -c -m 644 ./adminpack--1.0.sql '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'</div>
<div>make: *** [install-world-contrib-recurse] Error 2</div>
<div><br>
</div>
<div>$ sudo mv /Library/Frameworks/Python.framework /Library/Frameworks/pfx</div>
<div><br>
</div>
<div>$ brew install postgresql</div>
<div>==> Downloading <a href="http://ftp.postgresql.org/pub/source/v9.2.3/postgresql-9.2.3.tar" target="_blank">
http://ftp.postgresql.org/pub/source/v9.2.3/postgresql-9.2.3.tar</a></div>
<div>Already downloaded: /Users/curtis/Library/Caches/Homebrew/postgresql-9.2.3.tar.bz2</div>
<div>==> Patching</div>
<div>patching file src/pl/plpython/Makefile</div>
<div>patching file contrib/uuid-ossp/uuid-ossp.c</div>
<div>==> ./configure --prefix=/Users/curtis/brew/Cellar/postgresql/9.2.3 --datadir=/U</div>
<div>==> make install-world</div>
<div>/bin/sh ../../config/install-sh -c -m 755 adminpack.so '/Users/curtis/brew/Cellar/postgresql/9.2.3/lib/adminpack.so'</div>
<div>/bin/sh ../../config/install-sh -c -d '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension'</div>
<div>/bin/sh ../../config/install-sh -c -m 644 ./adminpack.control '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'</div>
<div>/bin/sh ../../config/install-sh -c -m 644 ./adminpack--1.0.sql '/Users/curtis/brew/Cellar/postgresql/9.2.3/share/postgresql/extension/'</div>
<div>make: *** [install-world-contrib-recurse] Error 2</div>
<div><br>
</div>
<div>$ sudo mv /Library/Frameworks/pfx /Library/Frameworks/Python.framework</div>
<div><br>
</div>
<div>$ brew doctor</div>
<div>Warning: Your Homebrew is not installed to /usr/local</div>
<div>You can install Homebrew anywhere you want, but some brews may only build</div>
<div>correctly if you install in /usr/local. Sorry!</div>
<div><br>
</div>
<div>(Note: the logs above do not include another failure I had when installing berkeley-db46.)</div>
<div><br>
</div>
<div>[4] Selected logs from OMERO Linux installation:</div>
<div><br>
</div>
<div>
<div>$ omero config get <a href="http://omero.db.name/" target="_blank">omero.db.name</a></div>
<div>********************************************************************************</div>
<div><br>
</div>
<div> ERROR: Could not import omero.cli! (No module named omero.cli)</div>
<div><br>
</div>
<div> This means that your installation is incomplete. Contact</div>
<div> the OME mailing lists for more information:</div>
<div><br>
</div>
<div> <a href="http://www.openmicroscopy.org/site/community" target="_blank">
http://www.openmicroscopy.org/site/community</a></div>
<div><br>
</div>
<div> If you are building from source, please supply the build log</div>
<div> as well as which version you are building from. If you</div>
<div> downloaded a distribution, please provide which link you</div>
<div> used.</div>
<div> </div>
<div>********************************************************************************</div>
<div><br>
</div>
<div> Debugging Info:</div>
<div> --------------</div>
<div> CWD=/home/curtis/code/ome/openmicroscopy</div>
<div> VERSION=2.7.3 (default, Aug 1 2012, 05:14:39) [GCC 4.6.3]</div>
<div> OMERO_HOME=/home/curtis/code/ome/openmicroscopy</div>
<div> 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']</div>
<div><br>
</div>
<div>To fix, I needed to set OMERO_HOME to "openmicroscopy/dist" subfolder, so it could find the Python libs in lib.</div>
<div><br>
</div>
<div>It would be good to add this as a note to both of the walkthrough guides, in the "Developer server" section.</div>
<div><br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br>
</blockquote>
</div>
<br>
<div>
<div style="word-wrap:break-word"><span class="Apple-style-span" style="border-collapse:separate; color:rgb(0,0,0); font-family:Helvetica; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; orphans:2; text-indent:0px; text-transform:none; white-space:normal; widows:2; word-spacing:0px; font-size:medium">
<div style="word-wrap:break-word">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</div>
<br>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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