Installing Omero with Docker

Dear,

At the moment I am trying to install Omero, as it looks like a great system for image data management.
If I understand it correctly, there are multiple ways to install Omero. One of them is with Docker as described here: https://ome.github.io/training-docker/10-officialomero/. For this proof-of-concept, I decided to just use the default settings and use the script as is. So a docker container is running for the postgressSQL server, Omero-serber and the Omero-web app.

docker network create my-omero-network
docker run -d --name my-db-server --network my-omero-network -e POSTGRES_USER=omero -e POSTGRES_DB=omero -e POSTGRES_PASSWORD=SeCrEtPaSsWoRd postgres:9.6
docker run -it --rm centos ping my-db-server

docker run -d --name my-omero-server --network my-omero-network -e CONFIG_omero_db_host=my-db-server -e CONFIG_omero_db_user=omero -e CONFIG_omero_db_pass=SeCrEtPaSsWoRd -e CONFIG_omero_db_name=omero -e ROOTPASS=omero-root-password -p 4063:4063 -p 4064:4064 openmicroscopy/omero-server:5.4.0
docker logs -f my-omero-server

docker run -d --name my-omero-web-standalone --network my-omero-network -e OMEROHOST=my-omero-server -p 4081:4080 openmicroscopy/omero-web-standalone:master
docker logs -f my-omero-web-standalone

The docker-containers are running, and when visiting the http://localhost:4081 the login-page occurs. However, I was wondering which of the logins is actually the one to be used. As there are multiple, as so far I did not manage to login yet.
Any other input to make Omero work is welcome too, and thanks in advance for helping. I can share the docker-logs if that helps.

Kind regards,

Ah, interesting that you found that. Do be aware that OMERO 5.4 is now quite old. For a more up-to-date example, you might take a look at https://github.com/ome/docker-example-omero – It should always be using the latest releases.

Based on your settings here, you should be able to login as the admin user root with the password omero-root-password.

~Josh

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Dear Josh,

Thanks a lot.
Indeed. I got it to work with:

git clone https://github.com/ome/omero-deployment-examples/
sudo docker-compose up -d
sudo docker-compose logs -f

And could login with the password.

In the docker-compose.yml I saw that the SQLdatabase is stored by default at: /var/lib/postgresql/data. Is that correct? Then I will try to import and export some images.

Kind regards,

Hi @Tkranen,

Yes, that is the location specified by http://hub.docker.com/_/postgres

~Josh

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Thanks a lot.
I will check the postgress-docker out on how to set up the image database and importing images.

Hmmm… we might should take this to another thread here, but I think I have caused some confusion. There’s an overlap between Docker’s “images” and OMERO’s “images”.

The Postgres container isn’t responsible for OMERO images. It’s just something used to stored metadata. Once you have all the containers up and running locally, you can connect to OMERO as “localhost”. You can follow the desktop guide from https://omero-guides.readthedocs.io/en/latest/upload/docs/import.html to import OMERO images.

Hope that helps.
~Josh

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Hi Josh,

Thanks a lot. I just downloaded the OMERO.insight-5.5.11.zip, and it works like a charm. Thanks for all the help so far.

Kind regards,

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