Open Microscopy Environment

I am trying to install Omero 4.3 server in a PC using Ubuntu natty narwhal OS.

The install goes wrong at this step:
bin/omero config set omero.db.name 'myDatabase'

Please help!!

****
ERROR: Could not import omero.cli! (No module named omero.cli)

This means that your installation is incomplete. Contact
the OME mailing lists for more information:

https://www.openmicroscopy.org/site/community

If you are building from source, please supply the build log
as well as which version you are building from. If you
downloaded a distribution, please provide which link you
used.

********************************************************************************

Debugging Info:
--------------
CWD=/home/maria/Desktop/omero.server
VERSION=2.7.1+ (r271:86832, Apr 11 2011, 18:13:53) [GCC 4.5.2]
OMERO_HOME=/usr
PYTHONPATH=['/usr/lib/python', '/usr/var/lib', '/home/maria/Desktop/omero.server/bin', '/usr/lib/pymodules/python2.6', '/home/maria/Desktop/omero.server', '/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/pymodules/python2.7/gtk-2.0', '/usr/lib/python2.7/dist-packages/gst-0.10', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7', '/usr/lib/pymodules/python2.7/ubuntuone-client', '/usr/lib/pymodules/python2.7/ubuntuone-control-panel', '/usr/lib/pymodules/python2.7/ubuntuone-storage-protocol', '/usr/lib/fallback']

Hi,

We have just been working on a step-by-step install guide for Debian (including Ubuntu) and I believe it's ready for use, so I've just made it public.
http://www.openmicroscopy.org.uk/site/s ... alkthrough

You could either see if you've missed any significant steps, or just start from scratch?
By copying and pasting the commands in (adjusting some config to your preferences) it should be fairly straight-forward.

Hope that helps,

Will.

Also, how did you install IcePy?
~Josh.

Hello,
So I started over and followed the instructions of the Debian/Ubuntu installation from scratch.

I am still getting stuck on the configuration of OMERO.

ERROR: Could not import omero.cli! (No module named Ice)

This means that your installation is incomplete. Contact
the OME mailing lists for more information:

https://www.openmicroscopy.org/site/community

If you are building from source, please supply the build log
as well as which version you are building from. If you
downloaded a distribution, please provide which link you
used.

********************************************************************************

Debugging Info:
--------------
CWD=/home/maria/apps/OMERO
VERSION=2.7.1+ (r271:86832, Apr 11 2011, 18:13:53) [GCC 4.5.2]
OMERO_HOME=/home/maria/apps/OMERO/OMERO.server
PYTHONPATH=['/home/maria/apps/OMERO/OMERO.server/lib/python', '/home/maria/apps/OMERO/OMERO.server/var/lib', '/home/maria/apps/OMERO/OMERO.server-Beta-4.3.1/bin', '/usr/lib/pymodules/python2.6', '/home/maria/apps/OMERO', '/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/pymodules/python2.7/gtk-2.0', '/usr/lib/python2.7/dist-packages/gst-0.10', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7', '/usr/lib/pymodules/python2.7/ubuntuone-client', '/usr/lib/pymodules/python2.7/ubuntuone-control-panel', '/usr/lib/pymodules/python2.7/ubuntuone-storage-protocol', '/home/maria/apps/OMERO/OMERO.server/lib/fallback']

Based on Josh's comment I am guessing the problem lies with IcePy but don't know how to fix it.

I'd greatly appreciate any help you can provide!

Maria

Hi Maria,

I think that first we need to establish whether Ice is properly installed on your machine. If you could please execute the following command:
dpkg -s zeroc-ice33
& paste the output into a reply. This should at least tell us whether Linux thinks that Ice is installed.

We can also double check by visiting /usr/lib/pymodules/python2.7/ and listing the contents of the folder. We should see many entries containing the word Ice or Glacier. If you do then that is good.

So, assuming that Ice is installed we can look to see whether the python interpreter is finding the Ice libraries. If you execute the following command:

python -c "import IcePy"

& Ice is installed properly then we should not get any output, i.e. Linux is only telling us if something went wrong. If you do get output then please paste it into a reply.


Assuming that Ice is correctly installed & that python can find it then we need to look at environment variables. Could you supply the contents of your .bashrc file?

It would also help if you could tell me whether this is the 32bit or 64bit version of Ubuntu, and whether it is the server or desktop version.

Also you mentioned that this is a fresh install of OMERO. By this do you mean a fresh install of OMERO into a fresh Ubuntu install or one that you have already been using?

Sorry for all the questions, but the more information I have to work with the more help I can be.

Simon

Hi All,

Thank you! I ran the 'dpkg -s zeroc-ice33' command and it was clear that Linux didn't think Ice was installed.
I went back to the long command and installed only zeroc-ice33 again. Then everything else involving the server worked and it is running.

However, when I installed the OMERO.client, I can't loggin. It won't recognize either U: root P: omero nor U: omerouser P: omeropass to start the client. Any suggestions as to were I went wrong there? (or how I can find out what username & password it is looking for and/or change the password).

Thanks again,

Maria

Hi Maria,

the password you need is the one you passed to: "bin/omero db script" during "Installation". If you've forgotten what you entered, you can reset the password as described under "Passwords".

For more general information about the different passwords, see "Which password do I use where?".

Hope that helps.

Cheers,
~Josh.