[ome-users] PYTHONPATH

Sat Dec 12 17:25:36 GMT 2009

Hi,

This page has some easier instructions for Mac, which may help with  
PYTHONPATH issues.
http://www.openmicroscopy.org.uk/site/support/omero4/server/install-omero-4.1-on-mac-os-x-10.5
It describes editing the .bash_profile which achieves much the same  
as .bashrc.

The nano .bashrc command described below should be run when you are in  
the /User/user_name/ directory (on a Mac at least). Not sure how that  
relates to Unix.

> I ran echo $PYTHONPATH and got '/opt/Ice-3.3/python:

Just make sure that is the right path. Not
/Ice-3.3.1/
since you say you are using Ice-3.3.1 ?

  Hope that helps,

   Will.

On 12 Dec 2009, at 16:59, John Wallach wrote:

> I can't speak to whether you can upgrade directly but you should be  
> able to make sure your pythonpath is set correctly pretty easily.  
> Edit the .bashrc with whatever edit you are comfortable with (nano  
> or pico are good choices if you are not familiar with any) with the  
> command:
> nano .bashrc
> then add:
> export PYTHONPATH=$PYTHONPATH:/home/omero_user/omero_path/lib/python/
> to the file.
>
> jmw
>
> On Sat, Dec 12, 2009 at 5:15 AM, Gordon W. Laurie <glaurie at virginia.edu 
> > wrote:
> We are having an apparent PYTHONPATH issue (see thread below) and  
> have the suggestion from Ruben to edit our /home/@user/.bashrc file  
> then add an export PYTHONPATH line.
>
> Two questions:
> 1. Having a limited working knowledge of Unix, how do we edit this  
> file?
> 2. Since we are running OMERO 4.0.3 and Python 2.5.1, should be  
> first do upgrades on both, then work out problems later.  Can we  
> upgrade directly from OMERO 4.0.3 to 4.1.1?
>
> Gordon.
>
>
>
> Begin forwarded message:
>
> From: Ruben Bernardo Alves <rubenalves at fm.ul.pt>
> Date: December 11, 2009 8:36:05 PM EST
> To: "Gordon W. Laurie" <glaurie at virginia.edu>
> Subject: Re: [ome-users] ImportError: No module name Ice2
>
> I don't know, try to post this question on the OMERO forum.
>
> Cheers
>
> -----"Gordon W. Laurie" <glaurie at virginia.edu> wrote: -----
>
> To: » Ruben Alves <rubenalves at fm.ul.pt>
> From: "Gordon W. Laurie" <glaurie at virginia.edu>
> Date: 12/11/2009 08:05PM
> Subject: Re: [ome-users] ImportError: No module name Ice2
>
> Dear Ruben:
>
> I note that you are using Python2.6.  Would it make sense to upgrade  
> now to
> the latest Python (Python 2.6.4), and to Omero 4.1.1?  Then work out  
> any
> problems later.  Can I go upgrade to the latter directly from 4.0.3?
>
> Gordon.
>
>
>
> On Fri, 11 Dec 2009 10:20:17 +0000
>  » Ruben Alves <rubenalves at fm.ul.pt> wrote:
> OK, try to edit your /home/@user/.bashrc, and at the end add the  
> following line:
> export PYTHONPATH=/usr/lib/pymodules/python2.6/:/opt/Ice-3.3/ 
> python/:/@your_OMERO_path/lib/python/:/usr/local/lib/python2.6/:/usr/ 
> lib/python2.6/
>
> There are severals path for python lib, I was able to run  
> "something" only with long path.
>
> note: I'm running Omero 4.1.1
>
> Cheers
>
>
>
>
> Gordon W. Laurie wrote:
> Thanks, I ran echo $PYTHONPATH and got '/opt/Ice-3.3/python:'.  I  
> assume this indicates an okay path. Below is the Python info.
>
> Gordon.
>
> Python 2.5.1 (r251:54863, Feb  6 2009, 19:02:12)
> [GCC 4.0.1 (Apple Inc. build 5465)] on darwin
>
>
>
>
> On Thu, 10 Dec 2009 19:21:11 +0000
>  Ruben Bernardo Alves <rubenalves at fm.ul.pt> wrote:
> Hi Gordon,
> Did you check your $PYTHONPATH ?
> ex: echo $PYTHONPATH
>
> note: maybe a python update could break the links or the path.
>
> Cheers
>
>
> -----ome-users-bounces at lists.openmicroscopy.org.uk wrote: -----
>
> To: ome-users at lists.openmicroscopy.org.uk
> From: "Gordon W. Laurie" <glaurie at virginia.edu>
> Sent by: ome-users-bounces at lists.openmicroscopy.org.uk
> Date: 12/10/2009 07:15PM
> Subject: [ome-users] ImportError: No module name Ice
>
>  Upon restarting OMERO, I am encountering 'ImportError: No module  
> named Ice'.  Have OMERO 4.0.3 running and Ice 3.3.1.
>
> Any suggestions?
>
> Gordon.
>
>
>
> Gordon W. Laurie, PhD
> Associate Professor
> Department of Cell Biology
> Director, Biotechnology Training Program
> University of Virginia
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> Gordon W. Laurie, PhD
> Associate Professor
> Department of Cell Biology
> Director, Biotechnology Training Program
> University of Virginia
>
>
>
> -- 
> Ruben Alves System Analyst USI @ Instituto de Medicina Molecular
> Edifício Egas Moniz Av. Prof. Egas Moniz 1649-028 Lisboa Portugal  
> tel: 217999411 ext 47026
> rubenalves at fm.ul.pt
>
>
>
>
>
>
> Gordon W. Laurie, PhD
> Associate Professor
> Department of Cell Biology
> Director, Biotechnology Training Program
> University of Virginia
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