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 ` 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:`command-line-interface`. 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:`command-line-interface`. You will need to login as the 'omero' user to access the OMERO CLI (user: "omero" / pw: "omero"). Logout using Ctrl-D.