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Last pushed: 2 months ago
Short Description
Multi-container OMERO
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OMERO.grid Docker

This is an example of using OMERO on multiple nodes (such as running the Processor service on a separate node from the main OMERO.server), based on
http://www.openmicroscopy.org/site/support/omero5/sysadmins/grid.html#nodes-on-multiple-hosts

Building the images

./build.py omero-grid
./build.py omero-grid-web

This will automatically build and tag the images as openmicroscopy/omero-grid:latest and openmicroscopy/omero-grid-web:latest.

Running the images

To run the Docker images start a postgres DB:

docker run -d --name postgres -e POSTGRES_PASSWORD=postgres postgres

Then either run a single all-in-one master:

docker run -d --name omero-master --link postgres:db -e DBUSER=postgres \
    -e DBPASS=postgres -e DBNAME=postgres -p 4063:4063 -p 4064:4064 \
    openmicroscopy/omero-grid master

Or run a master and one or more slaves, the configuration must be provided to the master node.
For example, to run two Processors on separate slaves and all other servers on master:

docker run -d --name omero-master --link postgres:db -e DBUSER=postgres \
    -e DBPASS=postgres -e DBNAME=postgres -p 4063:4063 -p 4064:4064 \
    openmicroscopy/omero-grid master \
    master:Blitz-0,Indexer-0,DropBox,MonitorServer,FileServer,Storm,PixelData-0,Tables-0 \
    slave-1:Processor-0 slave-2:Processor-1
docker run -d --name omero-slave-1 --link omero-master:master \
    openmicroscopy/omero-grid slave-1
docker run -d --name omero-slave-2 --link omero-master:master \
    openmicroscopy/omero-grid slave-2

Finally run the web client:

docker run -d --name omero-web --link omero-master:master -p 8080:8080 \
    openmicroscopy/omero-grid-web

Configuration files

Additional configuration files for OMERO can be provided by mounting a directory /config inside any of the containers.
Files will be loaded with omero load.
For example:

docker run -d --link omero-master:master -v /config/master:/config:ro \
    openmicroscopy/omero-grid master

The OMERO.web nginx config file will be autogenerated at runtime if /etc/nginx/conf.d/omero-web.conf does not exist, so for example you can set a custom prefix in a file under /config and the template will be generated correctly.

If you want to manage the full nginx configuration outside Docker than mount /etc/nginx.

Default volumes

  • /home/omero/OMERO.server/var: The OMERO.server var directory, including logs
  • /OMERO: The OMERO data directory (omero-grid only)
  • /home/omero/nginx: Nginx var directory, including logs and cache files (omero-grid-web only)

Exposed ports

  • omero-grid: 4061, 4063, 4064
  • omero-grid-web: 8080

Example with named volumes

docker volume create --name omero-db
docker volume create --name omero-data

docker run -d --name postgres -e POSTGRES_PASSWORD=postgres \
    -v omero-db:/var/lib/postgresql/data postgres
docker run -d --name omero-master --link postgres:db -e DBUSER=postgres \
    -e DBPASS=postgres -e DBNAME=postgres -v omero-data:/OMERO \
    -p 4063:4063 -p 4064:4064 openmicroscopy/omero-grid master
docker run -d --name omero-web --link omero-master:master -p 8080:8080 \
    openmicroscopy/omero-grid-web

Running without links

As an alternative to running with --link the addresses of the database and master can be specified using the variables DBHOST and MASTER_ADDR.
This may be useful when running containers across multiple hosts.
For example:

docker run -d -e DBHOST=10.0.1.1 openmicroscopy/omero-grid master
docker run -d -e MASTER_ADDR=10.0.2.1 openmicroscopy/omero-grid-web

Custom OMERO builds

These images default to using the latest release build of OMERO.
You can override the version/branch, and/or the continuous integration server, see ./build.py --help for details.

The images will be tagged (<user>/<image>:<tag>) with a different user (based on the CI server if not the default) and tag (the release version or branch name) to indicate they are using a non-standard version of OMERO.

In addition omego args can also be passed, if this is done the image name will be prefixed with x-.

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Owner
joshmoore
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