[ome-devel] Matlab Integration with OME

[Tom Macura]

Hi,

You did almost everything right.

A CVS checkout basically is equivalent to an OME install package. You  
have to install OME (by running perl install.pl)
even after checkout.

So you have to check out into your home directory. e.g. /home/tmacur1  
or /home/guanghui
instead of / as you currently did.

Then you have to install by running sudo perl /home/tmacur1/OME/ 
install.pl

so now do

rm -rf /OME (To remove your current OME checkout -- it's in the wrong  
place)
cd /home/guanghui (to move to your home directory)
cvs -z3 -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome' checkout  
OME (to do a current checkout)
cd OME
sudo perl install.pl  (to install OME).

Let me know if you need more info or have further questions,

Tom


On May 30, 2006, at 5:13 PM, #HU GUANGHUI# wrote:

>
> Hi Tom,
>
> Thanks for the quick reply!
>
> As it is my first time using cvs, this is what i've done.
> (I'm using fedora core 3 in case the platform matters)
> As the root, under the "/" directory, i ran these commands:
>
> $ cvs -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome' login
> CVS password:anoncvs
> $ cvs -z3 -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome'  
> checkout OME
>
> Then the cvs did a lot of updating and checkout.
>
> Next I ran this, under "/OME" the directory where OME is installed
> $ cvs update -d
>
> However, i saw warning messages like the following
>
> cvs update: Updating conf
> cvs update: warning: cannot write history file /ome/CVSROOT/ 
> history: Permission denied
> cvs update: move away conf/httpd.ome.conf; it is in the way
> C conf/httpd.ome.conf
> cvs update: warning: cannot write history file /ome/CVSROOT/ 
> history: Permission denied
> cvs update: move away conf/httpd.omeds-dev.conf; it is in the way
> C conf/httpd.ome.conf
>
> and the list goes on...
> And when i did a "slocate CVSROOT", it was not able to find such  
> directory.
> So I was afraid I did something wrong, or misunderstand the  
> instructions.
>
> Also, I understand OME can be "reinstalled" if so how am I going to  
> perform the reinstallation?
> Is it by running the script "install.pl" that is found in the  
> directory of the installed OME?
>
> Thanks for your time, I'm also eager to get the integration up and  
> running.
>
> Cheers,
> GuangHui
>
> -----Original Message-----
> From: Tom Macura [mailto:tm289 at cam.ac.uk]
> Sent: Sun 5/28/2006 3:24 AM
> To: #HU GUANGHUI#
> Subject: Re: Matlab Integration with OME
>
> Hi GuangHui,
>
> If you want to use OME with MATLAB you really have no choice but to
> get the latest version of OME from CVS (info at
> cvs.openmicroscopy.org.uk).
> The current release (2.4.0) is over a year old. There have been many
> many improvements to the OME/MATLAB coupling.  A new release is in
> the pipeline but I have no idea when it will happen.
>
> The CVS version of OME is pretty good -- don't worry about bugs the
> MATLAB part is very thoroughly tested (because we use it all the time
> as infrastructure for our own research) Unfortunately they are always
> unknown problems.
>
> You might want to look at the paper I wrote about OME/MATLAB
> coupling:  http://www.openmicroscopy.org.uk/publications/
> MatlabHandler.pdf
>
> Hope things work for you. Don't hesitate to write back. I'm very
> excited you're interested in OME+MATLAB and want to help you,
>
> Best,
>
> Tom
>

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