Login to your AWS account

Choose EC2 from the AWS Console

Select Images (AMIs)
	
	From the dropdown public AMIs search GenomeVIP
	
Choose a server & runtime images

	Launch the server (most recent version is recommended) from the Actions menu
	
	Select Launch
		
	Choose an instance type (m1.medium recommended)
	
	Click "Next: Configure Instance Details"
	
	Select number of instances (at least 1)
	
	Select the network type, EC2 Classic
	
		NOTE: The Availability Zone should match the instance zone (and the Volumes Availability Zone should match)
		
	Skip the Storage & Tag tabs
	
	Go to tab 6, Configure Security Group
	
		Add a rule for HTTPS
	
	Review selections, and launch
	
	Choose the desired keypair (you can proceed without a key pair)
	
Go to your dashboard (orange box)

	Select EC2 to check its running as many instances as you chose above and *get the public IP*
	
To get to the GenomeVIP homepage, the site is https://publicip/~genomevip (where publicip is the public IP of a running instance, the site is case sensititve).

Select  either AWS or Local Cluster

If AWS

	Provide your AWS login credentials

	A session ID will be generated for future logins

If Local Cluster

	Provide your login credentials to your local cluster

Select either an EBS volume (only with AWS accounts), user defined, or 1000 Genomes

Click “Load list” to load the data

Choose the .bam files to use

Choose a reference genome

Select if you want a copy of all sorted .bam and .bai created to storage directory

Execution Profiles

	New

Select a Run mode (germline, somatic, de novo/ family trio)

Select Paramaters (these can be tuned further in each tool)

Existing

Upload from file

Select Genomic Regions

	No selection

	Standard chromosome1-22, X, Y

	Standard chromosomes plus contigs MT, GI, GL, NC

	User defined either manual entry or file upload

Click the “Apply Profile” button to apply above entries

Customization

	For each tool switched on by the run mode selected, fine tune any parameters. If necessary, turn off any tools switched on or turn on any tools not automatically selected.

If AWS

	Select an AWS computing resource instance

	Select a storage bucket to put results

If Local Cluster

	Select a local computing resource

Choose a working directory to run jobs

Select submit action (create script vs. execute script)

Specify any additional comments (optional)

Double Check

	Click the “Preview” button to check execution profile

	Click the “Validate” button to preview and check user settings

Click “Submit”

Check out the results by navigating to the location displayed (for both AWS and Local Cluster)

Enjoy!

Additional options and accounts management may be configured for AWS