Overview

This cookbook contains recipes for installing and configuring OMERO.server and OMERO.web.

Prerequisites:

If you deploy using Chef Solo, you need to set node['postgresql']['password']['postgres'] to a password for the database.
(By default, the postgres cookbook wants to persist a randomly generated password in a node attribute ... which only works in Chef Server mode.)
Refer to the postgres cookbook's README file for more details, and instructions on how to generate the password hash.

You need to open firewall access on ports 4063 and 4064 for OMERO.service, and optionally ports 80 and 443 for Omero.web. (If you use non-standard ports, adjust accordingly.)

For a NeCTAR virtual, you need to open the external firewall ports using the NeCTAR Dashboard:

1. Go to your project's "Access & Security" panel
2. Click "Edit Rules".
3. Click "Add Rule", fill in the port and then "Add".
4. Repeat for each port you need to open.

Recipes:

The omero::server recipe installs and configures OMERO.server according to the standard OMERO instructions.

The omero::web recipe runs the server recipe, and then installs and configures OMERO.web using Nginx as the front-end web-server.

The omero::web-internal recipe runs the server recipe, and then installs and configures Omero.web in development mode. (The omero-web service is disabled, and you need to run it by hand using ".../OMERO.server/bin/omero web start".)

Attributes:

The following attributes control the main OMERO installation recipe:

• node['omero']['release'] - The OMERO release to be installed. This can be either the URL for the OMERO.server downloadable, or its basename. Note that this recipe only supports 5.x releases.
• node['omero']['install'] - The OMERO installation directory; defaults to "/opt/omero". The installation will be created as a subdirectory of this, and an "OMERO.server" symlink will be created to the installation.
• node['omero']['user'] - The OMERO service user name; defaults to "omero".
• node['omero']['var'] - The OMERO server's 'var' directory; defaults to "/var/omero".
• node['omero']['db_user'] - The OMERO server's postgres database account name; defaults to "db_user".
• node['omero']['db_password'] - The OMERO server's postgres database account password; defaults to "db_password". THIS SHOULD BE CHANGED.
• node['omero']['db_name'] - The OMERO server's postgres database name; defaults to "omero_database".
• node['omero']['root_password'] - The OMERO root password; defaults to "omero_root_password". THIS SHOULD BE CHANGED.

The following attributes control the OMERO web recipes:

• node['omero']['web']['enabled'] - This tells the omero::web recipe to enable or disable the omero-web init script; defaults to true.
• node['omero']['web']['frontend'] - Select the frontend webserver.
  Currently, only 'nginx' is supported.
• node['omero']['web']['http_port'] - Select frontend webserver's HTTP port;
  defaults to 80.
• node['omero']['web']['recipe'] - Select the Chef recipe to use to install the frontend webserver. By default, we use the "standard" Chef Community cookbook.
• node['omero']['web']['configure'] - If true, the web recipe will attempt to configure the frontend webserver on the assumption that it only needs to support Omero.web. If false, we don't touch the frontend configuration.
  Defaults to true.

Starting and stopping services

The recipe installs service scripts in "/etc/init.d" so that you can start and stop the services. The "omero" script is for the OMERO.service services, and the "omero-web" script is for the OMERO.web services.

For example:

  $ sudo /etc/init.d/omero start      # starts the OMERO service
  $ sudo /etc/init.d/omero stop       # stops the OMERO service
  $ sudo /etc/init.d/omero restart    # stops and starts the OMERO service

Testing

If the OMERO.server installation is working, you should be use OMERO.client tools to talk to the server on (at least) port 4063 of the server, using the server's external IP address or hostname. (The OMERO.client tools can be downloaded and installed on Windows, Mac and Linux machines.)

If the OMERO.web installation is working, you should be able to access the OMERO web service using a web browser. Use "http:///" as the URL, where is the IP address of the server. (If you have configured the server to use a non-standard port, include that in the URL.)

In both cases, you can use the "root" account and password for initial testing.

More documentation

For more documentation, please refer to the relevant OMERO documention pages on their support site:

• http://www.openmicroscopy.org/site/support/omero5/

The installation documentation has various hints and links on checking things are working, and diagnosing problems:

• http://www.openmicroscopy.org/site/support/omero5/sysadmins/unix/server-installation.html

Limitations

The cookbook only works on Ubuntu 14.04 and Fedora 19/20 at the moment, and only supports 'nginx' as the webserver front-end.

I have tried to get 'apache' working on Ubuntu 14.04, but at this time the community cookbook for Apache2 does not support Apache 2.4. Since Apache 2.4 is the standard for Ubuntu 13.10 and Fedora 19+, that means the 'apache' won't work there either.

Fedora support requires a fix to the community "postgresql" cookbook. I've sent a pull request, but in the meantime you can get hold of the fixes by adding this line to your Berksfile, updating and re-vendoring.

cookbook 'postgresql', github: 'crawley/postgresql', branch: 'fedora16+fixes'

TO DO List

• We are not yet doing anything about backup or internal firewalls.
• We are not attempting to configure advanced options such as LDAP, OMERO.dropbox, though apparently OMERO.dropbox is running ...
• Support for Omero.web needs more work / testing
• Support more OS platforms
• Support for SSL i.e. generating and configuring a certificate
• Support for updating Omero
• Support for rerunning with different usernames, passwords, etc.
• Support for installing clients
• Support for apache frontends (depending on community cookbook updates).
• Support for updating postgresql(?).