Setup

A few basic things need to be set up before we can get to the actual work. In the interests of time and speed we have setup a You'll need to create and start a VM based on a snapshot we provide that has a lot of bioinformatics software pre-installed. As you know getting bioinformatics software installed is often a time-consuming task that we have done for you.

Create a VM based on the asm-ngs-workshop image.

1. Name your VM: asm-ngs- Use the user name from the email address you provided us to setup for the workshop
2. Change the Boot Disk
   1. Click Change
   2. Click Snapshots
   3. Click Snapshot and scroll down and select the snapshot called asm-ngs-workshop
   4. Click the blue Select button at the bottom of the window
3. Leave the rest of the options at their default values and click the blue Create button at the bottom of the window.

NEED SCREEN SHOTS HERE

Log into your new VM

It will take a few minutes to create the new VM. Once it is running click the SSH button to the right of the VM list.

NEED SCREEN SHOT HERE

Once you can log into that VM you should create a Cloud Storage Bucket for the workshop with the following command.

gsutil mb gs://asm-ngs-$USER

Now you need to configure the sra-toolkit.

vdb-config -i

NEED SCREEN SHOT HERE

** NEED THEM TO TEST A PREFETCH AND FASTERQ-DUMP OF SAY SRR000001