NIAGADS
  • VCPA
  • Introduction
  • Step 1: Set up the Amazon Web Services (AWS) environment
    • 1.1 Create AWS account
    • 1.2 Configure your computing environment and login to AWS
    • 1.3 Setup a S3 bucket (simple storage solution for AWS) for hosting sequencing data
    • 1.4 Install AWS command line software for accessing S3 bucket via command line interface
    • 1.5 Install StarCluster for AWS instance provisioning (optional)
  • Step 2: Create your tracking database instance
    • Option 1: Setup sample tracking database using Public AMI (recommended)
    • Option 2: Setup sample tracking database using Docker
  • Step 3: Configure your project information in the tracking database
    • 3.1 List all projects in the tracking database
    • 3.2 Create the project in the tracking database
  • Step 4: Upload sequencing data to your S3 bucket
  • Step 5: Configure your samples information in the tracking database
    • 5.1 Input the sample information to the tracking database
    • 5.2 Populate the tracking database with the S3 paths for the samples to be processed
    • 5.3 Populate the tracking database with the designated result folder for each sample to be processed
    • 5.4 Input PCR protocol information into the tracking database
    • 5.5 Add the capture kit information (WES sample only) into the tracking database
    • 5.6 Generate an ID to represent the capture kit information (WES sample only)
  • Step 6: Submit a job to process one whole genome (WGS) / whole exome (WES) sample
    • 6.1 Update vcpa-pipeline bitbucket contents
    • 6.2 Choose which workflow to use
    • 6.3 Enter your AWS credentials into the workflow script
    • 6.4 Launch Amazon EC2 Spot Instances via starcluster
  • Step 7: Review quality metrics of processed data
  • Step 8: Generating Project-level VCF via joint genotyping
  • Optional: Change software versions and dependencies of the VCPA workflow
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  1. Step 2: Create your tracking database instance

Option 1: Setup sample tracking database using Public AMI (recommended)

Using public AMI to setup the tracking database is easier, as the Starcluster is already pre-installed. Below are the step-by-step guide:

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Last updated 7 years ago

1) click "EC2 Dashboard" on your right. Then click "Launch instance" in blue to launch AMI

2) Click "Community AMIs" on the left panel, then type in "ami-acc840d3" in the search box. Then click select.

3) Next, choose the appropriate instance - we recommend using t2.micro for the tracking database of VCPA; as this is only used for hosting the database and submitting jobs. Click "Next: Configure Instance Details" on the bottom right hand corner to proceed.

4) Click "Next: Add Storage" on the bottom right hand corner to proceed.

5) Click "Next: Add Tags" on the bottom right hand corner to proceed.

6) Click "Next: Configure Security Group" on the bottom right hand corner to proceed.

7) Then open the public web port. Users need to configure the security group like "SSH" and "HTTP". Click "Review and Launch" on the bottom right hand corner to proceed.

8) Click "Launch" on the bottom right hand corner to proceed.

9) Finally, users can view the the Public DNS/ Public IP information. An example is shown in the "right box" in the figure below:

Users can then use this DNS/IP information to view the webpage of the tracking database by this URL: DNS/v1/projects, where users need to specify their own DNS/IP information. See figure below for an example:

After the server / instance is setup, users need to login to this tracking database server to configure the projects / samples information and submit jobs. Details will be discussed in Steps 3-6 of the gitbook documentation.

1) Please fill in your [your_ssh_key.pem], [DNS/Public_IP].

  $ssh -i ~/.ssh/[your_ssh_key.pem] ubuntu@[DNS/Public_IP]
  Are you sure you want to continue connecting (yes or no)? yes
  Welcome to Ubuntu 16.04.4 LTS (GNU/Linux 4.4.0-1052-aws x86_64)

2) Please add your [AWS_ACCESS_KEY_ID], [AWS_SECRET_ACCESS_KEY].

 $ sudo nano /var/www/seq-processing/.env

Alternatively, users can also view the webpage of the tracking database by the URL: "", where IP is the public IP information.

http://IP/v1/projects
Launch instance
Community AMIs(ami-acc840d3)
Instance Type
Configure Instance Details
Storage
Tags
Configure Security Group
Review Instance Launch
URL: DNS/v1/projects