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:
$ bin/omero help admin # same as bin/omero admin -h
In addition to the CLI commands which can be listed using
omero help --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 omero help command or the
omero help --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:
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
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:
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.