Open Microscopy Environment

Hello everyone I am Shane Klumpp,

I want to preface that I am extremely new to networking, as I am a bioinformatics intern so this isn't my main speciality. I have launched OMERO as an EC2 instance on Amazon Web Services and have questions regarding connecting to OMERO.

I can ssh into the instance normally and login as an OMERO user. I am wondering how i set up the networking capabilities to be able to connect over a webclient or though OMERO.insight

We use a static IP for the EC2 OMERO instance if that helps. I am stuck at this point and have searched across the forum/the omero websight for help but am coming up blank. Do I need to set up port forwarding through the CLI?

Looking for a little bit of direction.

Thank you for the help

Shane

Hi Shane

You'll need to ensure the following ports are open on your instance:

• web: 80, 443
• omero: 4063, 4064

Amazon has some instructions for modifying your access rules here: http://docs.aws.amazon.com/AWSEC2/lates ... tance.html

It's possible you'll need to edit the firewall rules inside your VM too.

If this doesn't help can you give us more information about your VM, including the operating system, and how you setup OMERO- did you follow a particular set of instructions?

Thanks, Simon

In terms of the second part of the question, the VM is just a standard OMERO ova. We're using it as a test case on AWS before we decide if we want to build our own OMERO. Standard Ubuntu 14.04 operating system. Nothing changed from the original OVA we used everything as a default.

For the security groups we already have some ports open (443 for instance). Does this need to be open for both SSH and TCP protocols?

If I needed to, how would I change the firewall rules within my OMERO system?

Sorry if this doesn't really make sense or if my wording is confusing, once again I am new to this. Thanks for all of your help Simon!

Shane

Hi Shane

Did you download the ova from https://downloads.openmicroscopy.org/omero/5.1.2/#va or somewhere else? We stopped producing prebuilt OVA images a while ago, and the 5.1 line is no longer supported. We've recently started working with Docker and OpenStack, and producing OMERO cloud images is on our todo list. In any case our old OVAs shouldn't have an active firewall.

What I'd recommend is starting from a fresh operating system image (either CentOS 7 or Ubuntu LTS), and follow one of the walk-throughs:

• http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/server-centos7-ice36.html
• http://www.openmicroscopy.org/site/support/omero5.2/sysadmins/unix/server-ubuntu1404-ice36.html

If you have any problems just post here.

Simon

Yes I downloaded it a couple of months ago from that link. We had been working with the OVA image locally and decided to try it with AWS.

The advantage to setting up our own OMERO server from scratch would be that it is continuously updated correct?

Thank you for your help

Shane

Hi Shane

The OMERO version in the OVA is out of date- we're no longer supporting it, so there will be several bugs which have been fixed in the current release (5.2.6, http://downloads.openmicroscopy.org/omero/5.2.6/). Originally we created the OVAs with VirtualBox but had to stop due to the work involved. As I've already mentioned we've since started using Docker and OpenStack internally, it's useful to know that you're using AWS because it means we can start to prioritise creating a production cloud image. Do you have any special requirements for using OMERO on AWS? If so I'll make a note of it so we can use it as a future test case.

The walk-through scripts I pointed you to are the easiest way to install OMERO if you don't have a lot of systems administration experience. If you do have a fair bit of experience the other option you could consider is Ansible, a configuration management tool. This is a tool we're using internally and it's almost production ready, though be aware we might need to make some breaking changes before we officially announce it. If you're familiar with this tool you basically need the "omero-server" role from https://github.com/openmicroscopy/infrastructure, and in all likelihood this is what we'd use to build our cloud images in future.

Simon