FW: [ome-users] Re: OME on MacOS 10.4.4

McCaughey, Michael J michael.j.mccaughey at Vanderbilt.Edu
Thu Jan 19 20:30:02 GMT 2006 

Installing OME on Mac OS X 10.4  (“Tiger”) from source, not Fink
(a/k/a “The Manly Way”)

Date: 10/12/05		Author: Mike McCaughey (mike.mccaughey at vanderbilt.edu)

About my system: This test install was done on a Dual 2.7GHz PowerPC G5 running Mac OS X 10.4.2

1)Start with a clean install from the Tiger DVD distribution, then install all the updates provided with the System Preferences Software Update feature. You are likely to need to restart the Mac and run Software Update a few times to get everything.

2)Install the Xcode Developer tools from the Apple Developer site (http://developer.apple.com/tools/xcode/)  and install. (Version 2.1)

3)Download the OME stable tarball from the OME site and untar in a suitable location.

4)Tiger as shipped is missing a number of libraries and perl modules needed for OME. Unfortunately, Fink does not have many libraries that work with 10.4, so we’ll have to get the sources and build them from scratch. You can download all of the necessary source tarballs and place them in a suitable location for installation (some prefer /usr/local/src for this, or you could use a simple folder placed in your own documents folder, but put them all in the same place).

5)First, you’ll need to get Term:ReadKey from CPAN. (Note: perl –MCPAN –e ‘install Term::ReadKey’ does not seem to work.) Term::ReadKey can be found at http://search.cpan.org/~jstowe/TermReadKey-2.30/ReadKey.pm (Version 2.30).  Gunzip, untar, and run perl Makefile.PL; make; sudo make install to install.  The OME installer script will not work at all until this is installed.

6)Running sudo perl install –l to list the libraries that are not installed. On my system, libpng, libjpeg, libtiff, libgd, and expat were not present. In addition, you’ll need zlib and freetype2 to get these libraries to build.

7)Libpng: Download from www.libpng.org (version 1.2.8)

8)Libjpeg: Download from www.ijg.org/files (version 6b)

9)Libtiff: The latest version of libtiff (3.7.2) does not appear to build correctly under Darwin. I used v3.5.7 from the OME site.  Download with curl –O http://openmicroscopy.org/packages/source/tiff-v3.5.7-osx-LZW.tar.gz.

10)Libgd: Download from http://www.boutell.com/gd (version 2.0.33)

11)Expat: Download from http://sourceforge.net/projects/expat (version 1.95.8)

12)Zlib: Download from http://www.zlib.net (version 1.2.3)

13)Freetype2: Download from http://freetype.sourceforge.net (version 2.1.10)

14)Uncompress and untar the downloads into your chosen src folder, they’ll create their own subfolders.

15)Go to the libjpeg folder and carefully read the INSTALL file. Pay attention to directory renaming and placement for libjpeg and zlib folders. If you fail to follow the instructions, it won’t work.

16)Go to the zlib folder and do ./configure; make; sudo make install

17)Go to libpng folder and do ./configure; make; sudo make install. Do sudo make test to see if it worked. It should.

18)Go to libtiff folder, do ./configure; make; sudo make install
19)Go to libjpeg folder. Do:  export DYLD_LIBRARY_PATH=/usr/local/lib
       Then ln –s `which glibtool` ./libtool
       Then ./configure –enable-shared; make; make test; sudo make install

20)Go to freetype folder, do ./configure; make; sudo make install

21)Go to gd folder, do sudo ln –s /usr/X11/include/fontconfig /usr/local/include/fontconfig
        Then ln –s `which glibtool` ./libtool
        Then ./configure; make; sudo make install

22)Go to expat folder, do ./configure; make; sudo make install

23)Go to the OME source folder, so sudo perl install.pl –l  This should show all libraries OK.

24)Now we need to install a few more things to make postgres and apache work with OME.

25)Readline: Download from http://directory.fsf.org/readline.html (version 5.0)

26)Gunzip,untar readline and cd to the readline folder.
Readline does not work with Darwin 8 without a minor edit: Do vi support/shobj-conf and search for the line containing darwin7*.  Change the 7 to an 8.
      Then ln –s `which glibtool` ./libtool
      Then ./configure; make; sudo make install

27)Postgres:  useful reading is OME Mac OS X install notes (Chris’s page), as well as Apple postgres page linked from Chris’s page.
      Download postgres from postgres.org (version 8.0.4). unzip, untar, and cd to the directory.  
      Do ./configure; make; sudo make install and ignore all the warnings gcc 4.0 spews.
      Make the user postgres on your mac as described on Chris’s page.
      Do sudo mkdir /usr/local/pgsql/data
      Do sudo chown postgres /usr/local/pgsql/data
      Do export PATH=$PATH:/usr/local/sbin
      Do echo $PATH and verify both /usr/local/sbin and /usr/local/bin are there.
      Take a moment to edit you .tshrc to make sure these are added to your path at login. You may also want to add the lines: 
               setenv PGDATA /usr/local/pgsql/data
               setenv PATH ${PATH}:/usr/local/sbin:/usr/local/bin:/usr/local/pgsql/bin
      Login as postgres: su –l postgres  (enter the password you used when you created the postgres user)
      Init the database: /usr/local/pgsql/bin/initdb –D /usr/local/pgsql/data
      Start the server:  /usr/local/pgsql/bin/pg_ctl –D /usr/local/pgsql/data

27)	Now it’s time to fix the Perl libraries.  Most of which are missing. Note the perl –MCPAN doesn’t seem to work so well, and the files in the OME repository are typically older versions.  Let’s build from scratch.
All of these libraries can be found using http://search.cpan.org.  All are installed the same way: download, unzip, untar, cd to folder, perl Makefile.PL; make; sudo make install
You will need:
DBI (version 1.48)
DBD::pg (Current version 1.43 does not work with OME, get 1.22 from search.cpan.org/~dwwheeler/DBD-Pg-1.22/)
HTML::Template (version 2.7)
IPC::Run (version 0.79)
Class::Accessor (version 0.22)
Class::Data::Inhertiable (version 0.04)
Exporter::Lite (version 0.01)
Universal::Exports (version 0.03)
GD (version 2.28)
HTML::Target (version 3.04)
LWP (version 5.083)
XML::NamespaceSupport (version 1.09)
XML::Soap (version 0.12)
XML::LibXML::Common (version 0.13)
XML::LibXML (version 1.58)
XML::Parser (version 2.34)
SOAP::Lite (version 0.60a)
XML::LibXSLT (version 1.58)

Install in the above order.

28)mod-perl is broken on Tiger. You must use mod_perl 1.x, as Tiger ships with apache version 1.3.33 and not 2.x.  You can get the latest 1.x version of mod_perl (version 1.29) from http://search.cpan.org/~goyer/mod_perl.  It won’t install without apache source code, so you’ll need that too.  You can get Apache 1.3.33 from http://www.tux.org/pub/net/apache/dist/httpd).  Unzip and untar apache, do not make anything in the apache directory!.  Unzip and untar mod_perl, cd to the mod_perl directory, and install (perl Makefile.PL; make sudo make install)

29)Finally, fix OME: cd to OME source directory, then vi src/C/omeis/OMEIS_Error.h and remove the line defining OMEIS_ERROR_STR

30)Ready?  Cd to OME directory, and sudo perl install.pl

All should be well. You will for the most part be able to use defaults, as noted in Chris’s page you should ignore the LDAP messages (hit y) that appear in the initial setup.

31)Done! Try it out.

Notes: OME isn’t a big fan of DHCP, at least without reverse DNS.  If you have this problem, enter your IP for the web site location. It’ll break once your lease expires, but at least you can use it until you convince the network folks to fix DNS or give you a static IP or both.  You’ll need to reinstall.
The email address for the default ome owner must be less than 50 chars. Since mac machine names do not have this limitation, you may possible have to change the suggested default.
 If you need to reinstall, or your first install crashes at some point after postgres ome database gets created, the commands:
  sudo apachectl restart
  /usr/local/pgsql/bin/dropdb ome
Can be your friend. Warning: they will blow away any data you have stored.




Michael J. MCaughey, PhD
Molecular Physiology and Biophysics
U9203 MRBIII
6-6175



-----Original Message-----
From: Jason Swedlow [mailto:jason at lifesci.dundee.ac.uk]
Sent: Thu 1/19/2006 1:15 PM
To: McCaughey, Michael J
Subject: Re: [ome-users] Re: OME on MacOS 10.4.4
 
Mike-

Good to hear from you-- I need to talk with you-- will email in the  
next few days.

Did you attach your doc??  Did not receive??

Thanks!

Jason

On 19 Jan 2006, at 19:05, McCaughey, Michael J wrote:

> Joel-
> I got it running awhile back and have some very rough documentation  
> on how to. I've attached it as a word doc.  Let me know if you need  
> additional help.
>
> Mike
>
>
> Michael J. MCaughey, PhD
> Vanderbilt University School of Medicine
> Molecular Physiology and Biophysics
> U9203 MRBIII
> 6-6175
>
>
>
> -----Original Message-----
> From: ome-users-bounces at lists.openmicroscopy.org.uk on behalf of  
> Jason Swedlow
> Sent: Thu 1/19/2006 12:13 PM
> To: Joël Spaltenstein
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: [ome-users] Re: OME on MacOS 10.4.4
>
> Hi Joel-
>
> What version of OME are you running??  Tell us a bit about the
> error.  I am pretty sure Ilya Goldberg's group has OME CVS running
> under 10.4.x.
>
> We are working towards a release of this code, so we don;t have to
> tell people to keep going for OME CVS.
>
> Cheers,
>
> Jason
>
>
> On 19 Jan 2006, at 17:15, Joël Spaltenstein wrote:
>
> > Hi,
> >
> > I'm trying to install the OME server on a mac running OS X 10.4.4. I
> > saw that as of May last year you guys hadn't gotten it running yet,
> > have you made any progress? I've spent a good part of the day  
> fighting
> > with the installer. I'm sure if I keep on fighting with it for a  
> while
> > longer I'll be able to figure it out, but I was wondering if you  
> would
> > have any tips for me.
> >
> > Thanks,
> > Joël
>
>
> **************************
> MSI/WTB Complex
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> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone (01382) 345819
> Intl phone:  44 1382 345819
> FAX   (01382) 348072
> email: jason at lifesci.dundee.ac.uk
>
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> Open Microscopy Environment: http://openmicroscopy.org
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**************************
MSI/WTB Complex
The University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 345819
Intl phone:  44 1382 345819
FAX   (01382) 348072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************



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