Amazon Snapshot

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You may run the pipeline software on a single instance we have created for you in AWS. You may also create your own AWS instance and run it there. You may also, of course, install and run the software on your own hardware.

Your first task is get an AWS account and keys so that you can use the AWS EC2 Console Dashboard (see https://console.aws.amazon.com/ec2/). From here you can launch instances prepared by others or create your own. We cannot assist in this step - Amazon has plenty of documentation. Once you are at the AWS EC2 Console Dashboard, you're ready to run the pipeline.


Launch Your First Instance

You'll need to know some details when launching an instance:

  • What Instance to launch. You have several choices
    • ami-be59d78e which is an instance we have prepared based on Ubuntu Server 12.04.1 LTS. It has all of our software installed.
    • Some other instance. The instance must run 64 bit software and is either Ubuntu of any version or Redhat/CentOS 6.3. You will also need to install the Pipeline software.
  • Instance size (memory and number of processors). The pipeline software will require at least 8GB of memory (type m1.large) and can use as many processors as is available.
  • Storage for the instance refers to the size for root (/) partition. This can be quite small, as little as 8GB should work. Of course if you intend to bring lots of other files/programs to the instance, you may want to increase this to something a bit larger (e.g. 30GB).


Prepare Your Instance

If you launched some other instance than the one prepared for our software, you will need to install the Pipeline software. This is quite simple - see debian package or red hat package. This should only take 15 minutes.

The last step is to organize your storage so you have enough space for the input sequence data and the output of the aligner and umake steps. This is described in more detail in Amazon Storage. If you are not using AWS, the process will be similar to that described above, but the details will vary based on your environment.

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