OMERO as Nextcloud Application running on Docker

Hi,

I was wondering if OMERO in general, or OMERO.web could be integrated into the Nextcloud as an application.
We use a Nextcloud Docker Container on a University Server in the Würzburg Imaging Group for data exchange.
It might be interesting to combine that.
Further, we intent to run a test omero.server container next to the nextcloud container on the same server.
Maybe you have a better suggestion to install a closer communication between both, instaed of a OMERO.web app in nextcloud.
I am happy about any kind of response.

Kind regards and greetings to the CIC-Research Group

Johannes Balkenhol
Universitätklinikum Würzburg

Hi Johannes

You’re probably aware of this, but for the benefit of everyone else the OME provides production Docker images for OMERO.server and OMERO.web:

For convenience you can use Docker-compose: https://github.com/ome/docker-example-omero

What are the requirements for integrating an application into Nextcloud?

Thank you very much for your reply.
I very much appreciate the OMERO docker container. I think this are very smart solution and we are about to testing the different container you mentioned.
However, I was curious if omero.web, omero.server could also run as an APP in nextcloud like this:
https://apps.nextcloud.com/
, as we use nextcloud for file exchange and group organization.
Nextcloud use’s MariaDB, therefore directly running a OMERO.server within nextcloud would be complex, but maybe OMERO.web could be integrated.
It might be interesting also in face of the popularity to set up a nextcloud app.

Kind regards

Johannes

Hi @JohannesBalkenhol

That is certainly interesting. We do not have much experience with nextcloud and we also have very limited bandwidth at the moment.

Do you have experience in setting up an nextcloud app?

Cheers
Jmarie

Hi @j.burel ,

thank you for your fast response. I am more slow in response.
Unfortunatelly, I have no experience in setting up a nextcloud app.
But, we ll see how this develops in future.

Best
Johannes

@JohannesBalkenhol,

Keep us posted!
~J.

Hi @JohannesBalkenhol & al. I was wondering if you thought of ‘simply’ using nextcloud to provide disk space to the users and interfacing that with omero’s Dropbox system (so more a backend than frontend integration). Is there a reason not to do that?

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Hi @glyg. Thanks for your response. Just to summarize. We indeed use a nextcloud container for files exchange, like teaching videos, research data, pictures other media within a research group. However, OMERO is very nice in exchanging especially research on microscopy, e.g. just to have a look on somebodies current Light Sheed Image of Bone Marrow.
For now, there is a server running nextcloud container and OMERO.server container in parallel (just test wise). I think they don’t have to necessarily communicate with each other, but just to link out, e.g. there are some nice expression data of bone marrow and I am interested in a related microscopy picture, or have a proteom of platelet and want to see platelet focused in microscopy picture (using ROI).
I think that is just an easy link out with sending some parameters (either from OMERO to nextcloud or nextcloud to OMERO, backend or frontend).
Maybe this is in the end the easier way than to create an OMERO app for nextcloud, using the same database.
I just thought it would by nice if nextcloud includes a little dropdown menu (as it has) with the option to link out to the parallel OMERO server, or as u suggested, to use OMERO DropBox to link out to nextcloud database.

Best

Johannes

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Thanks @JohannesBalkenhol that sounds really promising, I’d be interested to see how this plays out, please keep us posted! I was wondering if you use Nextcloud syncing / disk space managing capacities for the DropBox folder of your omero instance? Maybe the fact that the dropbox folder is write-once is a deal breaker because that would make data management too unreliable ?

Syncing nextcloud disk usage and OMERO DropBox sounds interesting, but for that you should have a closer look in the processes. Unfortunatelly, I am no expert for that, but Nextcloud is more on editing files on the fly, so probably right @glyg, the write-once assumption would end up colourful with nextcloud.
Maybe its the best to run both in parallel and simply link out.

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