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

Visit Manage sessions to get a basic overview of how user sessions are managed.

See also

Advanced import scenarios

In-place import

OMERO.dropbox

Command Line Interface as an OMERO client