Amazon EC2 instances

For users of the Amazon Cloud (Amazon Web Services), we used to provide a machine image (AMI) with a complete, functional zUMIs installation. Since the addition of all dependencies into the miniconda environment that comes with zUMIs, this is no longer necessary. Any newly created EC2 instances with Ubuntu or AWS Linux will be directly compatible when using zUMIs.sh -c

Below find the last updated AMI:

You can start your EC2 instance with zUMIs in the US East (N. Virginia) location (change this in the top right corner). If you need to use a different location, the AMI may be copied through the AWS console.

In the AWS Console, click on AMIs. Here, switch the search bar to Public images and find the zUMIs image by pasting

** ami-0f949a9d22bd09289** (AMI ID)

or

** zUMIs2.4.0f-hvm** (image name).

Klick the Launch button to start the instance. When selecting the instance type, remember STAR needs at least 30 Gb RAM for loading the genome index. Follow the assistant to launch the instance and you are good to go!

To use the new instance, connect to it through ssh. You will get instructions from Amazon if you click on the "Connect" button in the EC2 Dashboard. It should look like this:

ssh -i "your-key.pem" [email protected]

Once logged in, you can find the zUMIs installation in the following path of the EC2 instance:

~/programs/zUMIs/

The example dataset is found here:

~/barcoderead_HEK.1mio.fq.gz
~/cDNAread_HEK.1mio.fq.gz

The output of an example run is located in:

~/testrun/