[ome-devel] Omero and docker

[Harri Jäälinoja]

Hi all,

I'm also working on the same thing, been eyeing it for a while but 
started seriously last week. Here's my current progress:

https://github.com/hajaalin/fig-omero

I managed to split everything in separate containers and start the whole 
show with Fig. And I like the way to pass secrets, using ejson made by 
Shopify. The database part now starts from a pg_dump made in OMERO 4.4. 
Just today I got LDAP working.

My goal is to take this into production use, I think it'd make updates 
easier later on.

Please have a look and let me know what you think, it'd be great to have 
the setup verified by more people :)

Best,
Harri

On 15/01/15 16:01, Simon Li wrote:
> Hi Hadrien
>
> Thanks for your continued interest in this. We're still very much at 
> the investigative stage regarding how we're going to use Docker, and 
> due to other priorities not much has changed since your last email. 
> More answers in line...
>
> On 15 January 2015 at 11:08, Hadrien Mary <hadrien.mary at gmail.com 
> <mailto:hadrien.mary at gmail.com>> wrote:
>
>     Hi guys,
>
>     I created a Dockerfile some weeks ago :
>     https://github.com/hadim/docker-omero. The main purpose was to both
>     learn how to install OME and get some training with docker.
>
>     I am planning to install an OME server for our lab and I am not
>     satisfied with my Dockerfile since it's pretty limited and use only
>     one instance for everything (no separated database instance).
>
>     I noticed it exists two repositories which seem to be official and
>     used there : https://github.com/ome/docker and
>     https://github.com/omedocker/omedocker. I'd like to test these
>     dockerfiles to see if it can fit for production in my case.
>
>     My questions are:
>
>     - for what purpose are you using docker (testing, production, ci...) ?
>
>
> Initially CI/testing, especially with different versions of 
> dependencies and configurations, if this goes well then potentially 
> production too.
>
>     - what is the difference between both repos ?
>
>
> omedocker was the original repo designed to work with Docker Hub 
> (automated builds), from what I remember we couldn't use an 
> organisation repo because Docker Hub wanted privileged access to our 
> GitHub account instead of just a single repository (this may have 
> changed in the intervening time).
>
> It was forked into ome/docker so that it would fit in to our normal 
> workflow with multiple OME team members having commit access, and 
> being able to open pull-requests.
>
>     - which one should I use ?
>
>
> Probably ome/docker which is effectively our development repo, once 
> our infrastructure is fully setup the tentative plan is to push 
> releases to omedocker to be automatically built by Docker Hub.
>
>     - does a more complete documentation exist about how to use these
>     dockerfiles (currently I am reading Makefile as a documentation) ?
>
>
> As I mentioned earlier everything is still very much at an exploratory 
> stage. Once everything is stable it'll be fully documented. If you 
> want to build everything in ome/docker you can run something like:
>
> for docker in $(python graph.py --order)
> do
>     docker=$(echo $docker | cut -d: -f1)
>     cd $docker
>     failed=0
>     docker build -t openmicroscopy/$docker
>     cd ..
> done
>
> graph.py outputs out the dependencies between images. Alternatively if 
> you just want to build one image it should be easy to figure out the 
> dependencies for yourself by checking the Dockerfile FROM lines.
>
> There's a lot of stuff in the repo at the moment, some directly 
> related to OMERO, others related to our infrastructure. E.g. 
> omero-in-a-box is an all-in-one image, omero-grid was an early attempt 
> at setting up different OMERO components on separate images.
>
> If there's anything else you need to know just ask!
>
> Best wishes
>
> Simon
>
>     Thanks !
>
>     --
>     Hadrien Mary
>
>     Ph.D student in Biology
>     Tournier-Gachet Team
>     CNRS - LBCMCP - UMR 5088
>
>     Université de Toulouse - Bât. 4R3B1
>     118, route de Narbonne - 31062 Toulouse
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>
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>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
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