Open Microscopy Environment

I have struggled to understand the Ubuntu 16.04 instruction guide as most of the guide makes references to other guides, but ultimately it leads to a misunderstanding as how OMERO.web and OMERO.server differ.

To me atleast what I don't understand is why OMERO.web and OMERO.server both have the same directories built within them. Both have OMERO.server and OMERO.server-5.2.7-ice35-b40. So to my knowledge I don't know whether people are referring to bin/omero commands for the server or web client.

I have opted to use Docker which can deploy the server, web client, and PostgresSQL database all in one command. Hadrien Mary's repository https://github.com/hadim/docker-omero is exactly what I was looking for.

I start docker with the following command:

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mgitt@mgpc:~/workspace/omero/docker-omero$ docker-compose up
Starting omero-data ...
Starting omero-data ... done
Starting omero-db ...
Starting omero-db ... done
Starting omero-server ...
Starting omero-server ... done
Starting omero-web ...
Starting omero-web ... done
Attaching to omero-data, omero-db, omero-server, omero-web
omero-db        | LOG:  database system was interrupted; last known up at 2017-10-13 14:46:57 UTC
omero-server    | Waiting for database server to be up.
omero-db        | FATAL:  the database system is starting up
omero-data exited with code 0
omero-db        | LOG:  database system was not properly shut down; automatic recovery in progress
omero-web       | 2017-10-13 15:04:08,570 CRIT Supervisor running as root (no user in config file)
omero-web       | 2017-10-13 15:04:08,572 INFO supervisord started with pid 1
omero-db        | LOG:  record with zero length at 0/20E6BF8
omero-db        | LOG:  redo is not required
omero-db        | LOG:  MultiXact member wraparound protections are now enabled
omero-db        | LOG:  database system is ready to accept connections
omero-db        | LOG:  autovacuum launcher started
omero-web       | 2017-10-13 15:04:09,574 INFO spawned: 'nginx' with pid 9
omero-web       | 2017-10-13 15:04:09,576 INFO spawned: 'omero_web' with pid 10
omero-web       | 2017-10-13 15:04:11,481 INFO success: nginx entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-13 15:04:11,481 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-13 15:04:12,292 INFO exited: omero_web (exit status 96; not expected)
omero-server    | ln: failed to create symbolic link 'lib/scripts/custom_scripts/omero_scripts': File exists
omero-web       | 2017-10-13 15:04:13,294 INFO spawned: 'omero_web' with pid 42
omero-web       | 2017-10-13 15:04:15,053 INFO success: omero_web entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
omero-web       | 2017-10-13 15:04:15,852 INFO exited: omero_web (exit status 0; expected)
omero-web       | 2017-10-13 15:04:15,889 INFO reaped unknown pid 64
omero-web       | 2017-10-13 15:04:15,889 INFO reaped unknown pid 65
omero-server    | No descriptor given. Using etc/grid/default.xml


What worries me is the 8th/7th to last lines that read:

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omero-web       | 2017-10-13 15:04:12,292 INFO exited: omero_web (exit status 96; not expected)
omero-server    | ln: failed to create symbolic link 'lib/scripts/custom_scripts/omero_scripts': File exists


If I presume everything is okay, I can open my browser to 0.0.0.0:80 and use root and password as described by Hadrien, but here is my output:


So now I'm stuck without a password. Anyone with docker experience may be able to read through the files and understand where the Dockerfile's have been set up incorrectly but I'm fairly new (2 days) to docker which is why I'm not sure how to fix the issue.

Hi Maxgitt,

Thanks for getting in touch!

Have you come across https://docs.openmicroscopy.org/omero/5 ... rview.html ? This page explains at least what OMERO.web is.

The Ubuntu 16.04 instruction guide refers to the Ubuntu 16.04 guides for installing OMERO.web two different ways. They don't link to any other guides that you don't need - just the Ubuntu 16.04 web guides.

Following https://docs.openmicroscopy.org/omero/5 ... ice36.html from top-to-bottom should be all you need to end up with a working OMERO server* - having made a decision about whether you deploy OMERO.web on the same server as the OMERO.server, or on a separate host.

Regarding the directory structures in OMERO.server and OMERO.web - that's because they can be independently deployed. Both the OMERO.web client and OMERO.server, e.g., can sit on separate machines, and both need to write logfiles, for example, and will do so to OMERO.server/var/log/ or OMERO.web/var/log. If you've taken the decision to deploy OMERO.web together with OMERO.server, they will both end up writing to the same directory - OMERO.server/var/log.

Hopefully someone else will be in touch with Docker related workflows - I can't help there.

Are you intending running a production resource with Docker?

* We were just told about one bug in the docs at viewtopic.php?f=5&t=8377 - where one step only should be run as root, rather than the OMERO operating sytem user. We'll be fixing that shortly.

All the best,

Kenny

Yes, I would like to run OMERO's (web+server) in production. I went through the Ubuntu installation from top -to-button and no luck. I had to wipe my computer to fix broken settings. Which is why I am a proponent of using docker. I can certainly take a look at the bug and try to reinstall in Ubuntu.

Hi Max,

We would think the Ubuntu walkthrough is the most straightforward method of getting you to a production instance - keeping in mind the one step which needs changed compared to the current version of the docs.

Adding Docker to the deployment is an increase in complexity - though as you say, it has it's benefits.

What might also be of interest is that there are "one step" installs of supported/current OMERO versions available via Ansible, but the OME project's public example is using CentOS, rather than Ubuntu. See https://github.com/ome/ansible-examples-omero

It's still important to know how to manage and tune the individual components, such as NGINX and PostgreSQL as well as OMERO even if automating the install, but that's at least one version of a "one step" deployment I've had personal experience of. Keep in mind that no install automation will in itself address aspects of running a production resource like e.g. handling backups.

You can contact the OME team via this forum, the mailing lists, or even IRC if you are having issues with the install at any point, cf https://www.openmicroscopy.org/support/

Best regards,

Kenny