System Administrator Documentation

This documentation begins with information aimed at OS-level administrators and moves on to day-to-day management of OMERO for facility managers (who may find it useful to read the Facility Managers walkthrough for an overview first).

Getting started

The OMERO server system provides storage and processing of image data which conforms to the OME Specification. It can be run on commodity hardware to provide your own storage needs, or run site-wide to provide a large-scale collaborative environment.

Although getting started with the server is relatively straightforward, it does require installing several software systems, and more advanced usage including backups and integrated logins, needs a knowledgeable system administrator.

Usage

You may find the OMERO clients overview user guide useful before working through the installation and maintenance guides provided in this section of the documentation.

Components

The server system is composed of several components, each of which runs in a separate process but is co-ordinated centrally.

• OMERO.blitz - the data server provides access to metadata stored in a relational database as well as the binary image data on disk.

• OMERO.dropbox - a filesystem watcher which notifies the server of newly uploaded or modified files and runs a fully automatic import (designed as the first implementation of OMERO.fs referred to in the architecture diagram).

• OMERO.processor - a process-launcher for running user-defined scripts.

• OMERO.tables - provide a way to efficiently store large, tabular results.

• OMERO.indexer - keeps a full-text search index up-to-date for searching.

If you are interested in building components for the server, modifying an existing component, or just looking for more background information, there is a section about the server within the Developer Documentation; the best starting point is the OMERO.server overview for developers.

Requirements & limitations

• What’s new for OMERO 5.6 for sysadmins
• Version requirements: supported platforms and versions
• System requirements: hardware specification and examples
• Example production server set-ups
• Known limitations

Installation

This section provides guidance on how to install and set up OMERO.server and OMERO.web on any of the supported UNIX and UNIX-like platforms. Following the installation links below you will find specific walkthroughs provided for several systems, with detailed step-by-step instructions. Reading through the OMERO.server installation and OMERO.web installation and maintenance pages first is recommended as this explains the entire process rather than just being a series of commands.

• OMERO.server installation
• OMERO.web installation and maintenance
• OMERO.server binary repository
• OMERO.server and PostgreSQL
• Installing additional features

Upgrading

Starting with OMERO 5.6, OMERO.server and OMERO.web installations are assumed to be separate throughout documentation, each with its own virtualenv. and installation directory.

• Migrate to a new operating system
• Migration to Python 3
• OMERO.server upgrade
• OMERO.web upgrade

Maintenance

This section contains instructions for administering, troubleshooting, and backing-up your installation.

• Troubleshooting OMERO
• OMERO.cli as an OMERO admin tool
• OMERO.server backup and restore
• OMERO upgrade checks
• Moving the data repository

Optimizing Server Configuration

This section discusses the options for configuring OMERO.server for optimum performance and security.

• Server security and firewalls
• LDAP authentication
• Performance and monitoring
• Search and indexing configuration
• FS configuration options
• Grid configuration
• Configuration properties glossary
• Syslog configuration

Managing OMERO

This section contains details on how to manage users, groups and data access in OMERO. New in OMERO 5.4.0, full administrators can now create restricted administrators to allow facility managers or other trusted users to carry out tasks on behalf of all users.

• Groups and permissions system
• Administrators with restricted privileges

See also

• Command Line Interface guides for User/group management and Changing ownership of objects

• Wlakthrough for Facility Managers

Data Import and Storage

This section contains details of how OMERO.fs allows you to import and store data with OMERO 5.

• OMERO.dropbox
• In-place import
• Advanced import scenarios

Optimizing OMERO as a Data Repository

This section explains how to customize the appearance and functionality of OMERO clients to host images for groups or public viewing.

• Publishing data using OMERO.web
  • Configuring public user
  • Full example of hosting data for a publication

• OMERO.web UI customization