Working with OMERO virtual appliance
------------------------------------
Now that your |VM| is up and running you have a choice about how to
interact with it.
- You can connect to OMERO.web from your host browser. Go to
http://localhost:8080/webclient.
- You can **use OMERO.clients from within your host OS.** This will
allow you to import data via a GUI and manage that data once
imported. To do so, download the :downloads:`OMERO.insight client <>`
and follow the instructions below. More information can be found on our
:help:`help website <>` which provides workflow-based guides to using the
OMERO.clients.
- Alternatively, you can interact with the server command line
interface by |SSH|'ing into the guest |VM| or by opening a console within
the |VM| itself. Administrators may need to use one of these methods to
restart the server and/or change configuration parameters. In this
case, you must have an |SSH| client installed on your host machine to use
to connect to the OMERO.server.
.. note::
The following examples assume that the OMERO |VM| is up and running on the
same machine that you are working on.
OMERO.web
^^^^^^^^^
Go directly to http://localhost:8080/webclient to log in with user:
"root" / pw: "omero".
.. note::
If you receive a 502 nginx error on first attempting to
connect to the web app on http://localhost:8080/webclient/ please
restart the virtual machine and try again.
OMERO.insight
^^^^^^^^^^^^^
You can run regular OMERO clients on your host machine and connect to
the server in the |VM|. Our example uses OMERO.insight running on Mac OS X
to connect to the |VM|.
- :downloads:`Download <>` and install OMERO.insight
- Start OMERO.insight
- Click the spanner icon situated above the password box to
enter the server settings box shown below.
.. figure:: /images/virtual-appliance-7server-addresses.png
:align: center
:figwidth: 45%
:width: 50%
:alt: Setting OMERO.insight server address and port number
Setting OMERO.insight server address and port number
- Use the *+* icon to add a new server entry with the address
*localhost* and the port *4064* then click apply
- You can now use the login credentials given above to log into OMERO.insight
using the login window shown below (user: "root" / pw: "omero").
.. figure:: /images/virtual-appliance-8login.png
:align: center
:figwidth: 45%
:width: 50%
:alt: OMERO.insight login window
OMERO.insight login window
- OMERO.insight should now load up and display the main window.
You can now use OMERO.insight to import and manage images on a locally running
virtual server just like you would use the standard remote server.
.. note:: A Getting Started guide is available for OMERO.insight on our
:help:`help website <getting-started-5.html>` if you need further
assistance to download and install the software.
Secure Shell
^^^^^^^^^^^^
You can log into your |VM| using |SSH|, allowing you to use the
:doc:`cli/index`.
In the following example, we assume that you have an |SSH| client installed
on your host machine and also that your |VM| is up and running.
You can log into the |VM| using the above credentials and the following
command typed into a terminal:
::
$ ssh omero@localhost -p 2222
This invokes the |SSH| program telling it to login to the localhost on
port 2222 using the username *omero*. Remember that earlier you set up
port forwarding to forward port 2222 on the host machine to port 22 (the
default |SSH| port) on the guest |VM|. You should be prompted
for a password. Once you have successfully entered your password, you
should be greeted by a prompt similar to the following:
::
omero@omerovm:~$
There are two potential complications to this method, (1) if you have
used a |VM| before then there could be old |SSH| fingerprints set up, (2)
the first time that you log into the |VM| you will be asked to confirm
that you wish to continue connecting. If you get the following message after
you invoke SSH, you need to remove the old fingerprints:
::
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that the RSA host key has just been changed.
The fingerprint for the RSA key sent by the remote host is
60:e0:d2:e8:fb:25:bf:09:53:9d:9d:59:59:45:cf:aa.
Please contact your system administrator.
Add correct host key in /Users/rleigh/.ssh/known_hosts to get rid of this message.
Offending key in /Users/rleigh/.ssh/known_hosts:14
RSA host key for localhost has changed and you have requested strict checking.
Host key verification failed.
You can do this using the following command typed into the terminal:
::
$ ssh-keygen -R [localhost]:2222 -f ~/.ssh/known_hosts
This should produce output similar to:
::
$ ssh-keygen -R [localhost]:2222 -f ~/.ssh/known_hosts
/Users/rleigh/.ssh/known_hosts updated.
Original contents retained as /Users/rleigh/.ssh/known_hosts.old
The first time that you log into the |VM| you will also be asked to
confirm that you wish to connect to this machine by a message similar to
the following:
::
$ ssh omero@localhost -p 2222
The authenticity of host '[localhost]:2222 ([127.0.0.1]:2222)' can't be established.
RSA key fingerprint is 60:e0:d2:e8:fb:25:bf:09:53:9d:9d:59:59:45:cf:aa.
Are you sure you want to continue connecting (yes/no)?
You should confirm that you wish to continue connecting, after which you
will be prompted for your password as usual:
::
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added '[localhost]:2222' (RSA) to the list of known hosts.
omero@localhost's password:
After which, you should have a prompt indicating
that you have a shell open and logged into the |VM|:
::
omero@localhost's password:
Linux omerovm 2.6.32-5-686 #1 SMP Mon Jun 11 17:24:18 UTC 2012 i686
The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.
Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Thu Apr 5 10:32:18 2012 from 10.0.2.2
omero@omerovm:~$ _
Log into the |VM| directly
^^^^^^^^^^^^^^^^^^^^^^^^^^
.. note::
Due to the frequent changes in the VirtualBox Guest
Additions, key mappings between the host and guest |OS| do not always
work. We recommend using |SSH| as the primary way of interacting with
the Virtual Appliance CLI.
When you start your |VM| using the VirtualBox GUI, as outlined above, a
window will be displayed showing the boot process for the machine as it
starts up, just like with a real piece of hardware. Once the boot
process has finished you will see a prompt displayed in this window like
so:
::
[System startup messages]
Debian GNU/Linux 6.0 omerovm tty1
omerovm login: _
You can log into the console of the |VM| directly using the user account
credentials above.
::
omerovm login: omero
Password: _
There is no GUI on the current OMERO virtual appliance so you will have
to use the Bash shell which looks like this:
::
omero@omerovm:~$ _
From here you can interact with OMERO.server via the
:doc:`cli/index`. You will need to login as the 'omero' user to
access the OMERO CLI (user: "omero" / pw: "omero"). Logout using Ctrl-D.