Note

This documentation is for the new OMERO 5.2 version. See the latest OMERO 5.1.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.

Overview

Command line help

The CLI is divided into several commands which may themselves contain subcommands. You can investigate the various commands available using the -h or --help option:

$ bin/omero -h

Again, you can use -h repeatedly to get more details on each of these sub-commands:

$ bin/omero admin -h
$ bin/omero admin start -h

The omero help command can be used to get info on other commands or options.

command

Display the information on a particular command:

$ bin/omero help admin       # same as bin/omero admin -h

In addition to the CLI commands which can be listed using --list, omero help can be used to retrieve information about the debug and env options:

$ bin/omero help debug     # display help about debugging options
$ bin/omero help env       # display help about environment variables

--all

Display the help for all available commands and options

--recursive

Recursively display the help of commands and/or options. This option can be used with either the command or the --all option:

$ bin/omero help --all --recursive
$ bin/omero help user --recursive

--list

Display a list of all available commands and subcommands

Command line workflow

There are three ways to use the command line tools:

1. By explicitly logging in to the server first i.e. by creating a session using the omero login command, e.g.:

   $ bin/omero login username@servername:4064
   Password:
   

   During login, a session is created locally on disk and will remain active until you logout or it times out. You can then call the desired command, e.g. the omero import command:

   $ bin/omero import image.tiff
   

2. By passing the session arguments directly to the desired command. Most commands support the same arguments as omero login:

   $ bin/omero -s servername -u username -p 4064 import image.tiff
   Password:
   

   The --sudo option is available to all commands accepting connection arguments. For instance to import data for user username:

   $ bin/omero import --sudo root -s servername -u username image.tiff
   Password for owner:
   

3. By calling the desired command without login arguments. You will be asked to login:

   $ bin/omero import image.tiff
   Server: [servername]
   Username: [username]
   Password:
   

Once you are done with your work, you can terminate the current session if you wish using the omero logout command:

$ bin/omero logout