[ome-users] PYTHONPATH

Sat Dec 12 17:39:17 GMT 2009

Hi again,

Just read the rest of the thread, two points (one pedantic):

1. Did you install on OS X with macports? Make sure that the directories you
are adding to your PYTHONPATH variable exist, ie run "ls
/usr/local/lib/python" in a shell and make sure the directories you are
adding are present.

2. Will is right, it's been awhile since I wore my sysadmin hat and I messed
up the order of .bashrc and .bash_profile. Edit .bash_profile or just
.profile since those are processed when the shell is invoked
non-interactively while .bashrc is not.

Speaking of that, does anyone have startup scripts for omero? If not would
it be useful to add them to the package?
Cheers,
jmw

On Sat, Dec 12, 2009 at 9:25 AM, Will Moore <will at lifesci.dundee.ac.uk>wrote:

> 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
>>>>> _______________________________________________
>>>>> ome-users mailing list
>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>
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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
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
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