docker-omero

Set of Dockerfile to setup an OMERO.server. This project aims to be used in production.

But the main purpose of this project is to make you love running OMERO.server :-)

How to start your OMERO.server

Basics

You will need to install docker > 1.13.0 and docker-compose >= 1.11.0 (check with docker version).

To start OMERO, simply do :

mkdir omero/ && cd omero/
mkdir omero-data/
mkdir docker-omero/ && cd docker-omero/
wget https://raw.githubusercontent.com/hadim/docker-omero/master/docker-compose.yml
docker-compose up  # You can use the -d option to run in the background.

It will launch all services : PostgreSQL server, OMERO.server and OMERO.web.

Wait a minute so the server can initialize.

To connect to the server with the OMERO Insight client use localhost as a server address and 4064 (by default) for the port. You also need to enable the encrypted mode by clicking on the locker image on the login window.

To connect to the server with the OMERO.web client, go to https://localhost.

Default admin credentials are root and password. Don't forget to change the password !

By default ../omero-data will be used as OMERO data directoy.

Parameters

You can use environment variables to configure OMERO :

#export OMERO_WEB_PORT=80
#export OMERO_WEB_PORT_SSL=443
#export OMERO_SERVER_PORT=4064
#export OMERO_WEB_PORT_DEVELOPMENT=4080
#export OMERO_DATA_DIR=../omero-data
#export OMERO_WEB_USE_SSL=yes
#export OMERO_WEB_DEVELOPMENT=no

mkdir -p $OMERO_DATA_DIR

• OMERO_WEB_PORT (default=80) : port used to expose OMERO.web server in unsecure mode (http).

• OMERO_WEB_PORT_SSL (default=443) : port used to expose OMERO.web server in secure mode (https).

• OMERO_SERVER_PORT (default=4064) : port used to expose OMERO.server. This port needs to be used when using the desktop client (OMERO Insight client).

• OMERO_WEB_PORT_DEVELOPMENT (default=4080) : port used to expose OMERO.web server in development mode.

• OMERO_DATA_DIR (default=~/data_omero) : data directory path on host used to store all data relative to OMERO.server.

• OMERO_WEB_USE_SSL (default=yes) : wether to launch OMERO.web with SSL mode (https), certificates are generated automatically or can be customized in $OMERO_DATA_DIR/web_certs.

• OMERO_WEB_DEVELOPMENT (default=no) : launch OMERO.web in development mode.

Add custom applications to a server in production

Create a folder in $OMERO_DATA_DIR/omero_web_apps. Inside write a file called deploy.sh which will be called before launching the OMERO.web server. For example to install the figure application (http://figure.openmicroscopy.org), put this in deploy.sh :

export PYTHONPATH=$OMERO_WEB_DEVELOPMENT_APPS:$PYTHONPATH

pip install reportlab markdown
./bin/omero config append omero.web.apps '"figure"'
./bin/omero config append omero.web.ui.top_links '["Figure", "figure_index", {"title": "Open Figure in new tab", "target": "figure"}]'

Don't forget to download the application to $OMERO_DATA_DIR/omero_web_apps.

Add custom configuration to a server in production

Edit or create the file $OMERO_DATA_DIR/config.sh. If it exists, it will be called before the server startup.

cat $OMERO_DATA_DIR/config.sh
./bin/omero config set omero.client.scripts_to_ignore '[]'

Add custom scripts to a server in production

All scripts inside $OMERO_DATA_DIR/omero_scripts will be available inside your OMERO.server. Technically $OMERO_DATA_DIR/omero_scripts is soft linked to lib/scripts/custom_scripts.

Advanced usage

You can launch only OMERO.server (and the database server of course) with this command :

docker-compose run --rm --name omero-server omero-server
# or use
make runserver

If you want to launch OMERO.web in development mode you can use the following commands :

export OMERO_WEB_DEVELOPMENT=yes

docker-compose run --rm --name omero-web omero-web
# or use
make runweb

You can enter in an already running container (OMERO.server or OMERO.web) with the following commands :

# For OMERO.server
docker exec -ti omero-server bash
# or use
make shellserver

# and for OMERO.web
docker exec -ti omero-web bash
# or use
make shellweb

Running OMERO.web in development mode

Developing an OMERO.web application

# Get OMERO.web shell and init the server
make runwebdev
su omero
bash /start_omero_web.sh
cd OMERO.server/
./bin/omero web start

You should now be able to connect to the dev server here http://127.0.0.1:4080.

Applications can be stored in /data/omero_web_apps ($OMERO_DATA_DIR/omero_web_apps on host).

Open a new shell.

make shellweb
su omero
cd OMERO.server/

./bin/omero config append omero.web.apps '"webtest"'
./bin/omero config append omero.web.ui.right_plugins '["ROIs", "webtest/webclient_plugins/right_plugin.rois.js.html", "image_roi_tab"]'
./bin/omero config append omero.web.ui.center_plugins '["Split View", "webtest/webclient_plugins/center_plugin.splitview.js.html", "split_view_panel"]'

In the first shell use Ctrl+C to stop the dev server.

export PYTHONPATH=$OMERO_WEB_DEVELOPMENT_APPS:$PYTHONPATH
./bin/omero web start

Your application should appear at http://localhost:4080/webtest.

Developing on OMERO.web itself

Coming soon !

Log

var directory (which contains logs) is symlinked to /data/omero_var ($OMERO_DATA_DIR/omero_var on host).

$ make datash
$ ls omero_var/log/
Blitz-0.log        FileServer.log     MonitorServer.log  Processor-0.log    master.err
DropBox.log        Indexer-0.log      PixelData-0.log    Tables-0.log       master.out

Backup and restore

You need to design a backup strategy according to your needs. All data needed to restart a server are located inside OMERO_DATA_DIR which is ../omero-data by default.

The server will automatìcally use data inside OMERO_DATA_DIR on startup.

About the images

omero-base: based on ubuntu:16.04, it contains omego and install OMERO.server.

omero-data: volume container based on busybox. /data is defined as a volume.

omero-db: based on postgres:9.4. It contains only few modifications from the original image.

omero-server: based on omero-base, it runs OMERO.server.

omero-web: based on omero-base, it runs OMERO.web.

See this schema for more details about how things are connected:

Authors

Hadrien Mary [email protected]

License

MIT License. See LICENSE.