Open Microscopy Environment

Hi team,

We would like to use OMERO CLI commands from our cluster nodes. So I'm wondering what the minimal requirements are to install that on the cluster nodes (ideally not requiring to bother the cluster administrator and doing everything in one's own environment?). The nodes run Centos 7 and the use conda for all virtual environment stuff.

Can this be done without requiring installing the full ZeroC Ice environment with yum? And is there a good way to install the zeroc-ice Python bindings in conda? Then it looks like OMERO.py has everything needed and that apparently can be installed in one's own directory.

Thanks,
- Damir

Hi Damir,

Have you seen https://bioconda.github.io/recipes/pyth ... EADME.html ?

That should do everything you want though the installation won’t be able to import.

~Josh

Thanks Josh,
Yes, a student had made me aware of that bioconda package but I hadn't used it myself yet. So that will work without doing a yum install of the "ice-all-runtime" stuff on the cluster node(s)? And would there then be a way to run the regular CLI commands such as "omero login xxxx" and "omero export xxxx"?
Cheers,
- Damir

Hi Damir

Unfortunately the python-omero BioConda package doesn't setup the CLI.

However it will automatically install all the OMERO.py dependencies so you could activate the conda env, then download and unzip OMERO.py in the usual way. Alternatively you could install only zeroc-ice.

I've just tested this in a clean environment using Docker and it looks like there's a bug: zeroc-ice on bioconda needs to be recompiled for the latest openssl. For now you can pin openssl to an older version:

Code: Select all

conda install -c bioconda -y 'zeroc-ice=3.6.*' 'openssl=1.0.*'
# omego is optional, you can download and unzip OMERO.py manually if you prefer
pip install omego
omego download python --sym auto
./OMERO.py/bin/omero version


Hi Damir,

I've just updated the bioconda package so that the following works for me:

Code: Select all

$ conda create -n omero -c bioconda python=2.7 python-omero
$ source activate omero
$ which omero
$ omero hql ...


All the best,
~Josh

Thanks Josh. I was able to test that and it works great.
Much appreciated,
- Damir