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:

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

Launch instance

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

Community AMIs(ami-acc840d3)

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.

Instance Type

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

Configure Instance Details

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

Storage

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

Tags

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.

Configure Security Group

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

Review Instance Launch

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:

URL: DNS/v1/projects

Alternatively, users can also view the webpage of the tracking database by the URL: "http://IP/v1/projects", where IP is the public IP information.

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