Skip to content

Getting Started with Millstone

Jump to bottom
mnapolitano89 edited this page Apr 10, 2014 · 25 revisions

This guide walks you through cloning the latest stable Amazon Machine Image (AMI) configured with Millstone. Most new users will want to use this guide. Docs for individuals wishing to configure their instance or modify source code are coming soon.

Prerequisites

You need to create to an Amazon Web Services (AWS) account. Brad Chapman's getting started guide for cloudbiolinux has a solid first chapter with instructions on getting everything setup. https://github.com/chapmanb/cloudbiolinux/blob/master/doc/intro/gettingStarted_CloudBioLinux.pdf?raw=true

Cloning the AMI

  1. In the EC2 console, navigate to Instances, then press the Launch Instance button. This will launch a wizard that walks you through setting up a new instance. The following steps provide instructions for configuring this instance.

  2. In the new instance wizard, choose the latest Millstone AMI. Make sure you're in the N. Virginia instance (upper right dropdown)

  3. On the 'Choose instance type' tab, select an instance according to your needs. We recommend m3.medium (select General Purpose on the left).

  4. In 'Configure instance', the only setting we recommend changing is explicitly setting the Availability Zone (we always use us-east-1a). You can only move EBS (Amazon hard-drives) between instances in the same zone, so it'll make things easier to consistently make everything in the same zone.

  5. In 'Add storage', increase the size of the root drive to the amount of space that you'll need. For bacterial genomes, about 2 GB per sample should be more than enough (i.e. 100 samples = 200 GB).

  6. In 'Tag instance', fill in an informative value for the 'Name' key. I like the name to include the date it was created and a description of what the instance is running (e.g. 2014_04_01_mutate_all_the_things).

  7. For security group, configure a group appropriate to your needs. Most users will want to create a security group with all of the following open (NOTE: This will make your instance publically visible, but login is still required.):

    • All ICMP
    • All TCP
    • All UDP
    • SSH

  8. Continue to the final tab where you'll press 'Launch the instance'. Select or create a key. If you create the key, download and save the private key. (NOTE: If you lose the private key there's no way to ssh back into your instance. You'll have to terminate it and create a new one.)

It takes about 5-10 minutes for the instance to launch and all bootstrapping to finished, after which your Millstone is ready to grind!

Accessing your instance

From the web, visit: ec2-xx-xx-xx-xx.compute-1.amazonaws.com (replacing the x's). This can be found by going to "Instances" and finding your created instance

To ssh in:

ssh -i ~/.ssh/your-key.pem ubuntu@ec2-xx-xx-xx-xx.compute-1.amazonaws.com
Clone this wiki locally