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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  • For Linux/MacOS Users
  • For Windows Users
  1. Step 2: Create your tracking database instance

Option 2: Setup sample tracking database using Docker

Start by installing docker-compose and downloading our sharing code

Download our sharing code:

 $ git clone --recurse-submodules https://bitbucket.org/NIAGADS/vcpa-web-api.git

Then go into the vcpa-web-api folder

 $ cd vcpa-web-api

and fill in the information to the .env file as shown below:

$ vi .envDB_NAME= ### tracking database nameDB_USER= ### tracking database user nameDB_PASSWORD= ### tracking database passwordDB_HOST= ### tracking database hostAWS_ACCESS_KEY_ID= ### AWS access key IDAWS_SECRET_ACCESS_KEY= ### AWS secret access keyAWS_REGION= ### AWS region

Users can verify their outcome by typing: docker-compose up; below is an example of what you will see

Successfully built af8f84acc855Successfully tagged gcadwebapi_web:latestRecreating gcadwebapi_web_1 ...Recreating gcadwebapi_web_1 ... doneAttaching to gcadwebapi_mysql_1, gcadwebapi_web_1mysql_1 | [Entrypoint] MySQL Docker Image 5.7.21-1.1.4mysql_1 | [Entrypoint] Starting MySQL 5.7.21-1.1.4web_1 | 172.18.0.1 - - [27/Mar/2018:18:05:55 +0000] "GET /index.php HTTP/1.1" 200 4

  • This docker instance has the web open to the public to allow remote analysis instances access to this API site.

  • Please ensure that this docker host has the default web port (80) accessible by public hosts.

For Linux/MacOS Users

  1. Make sure you turn off Firewall for private networks.

  2. This image version could directly build on Linux/MacOS.

For Windows Users

  1. Make sure you turn off Windows Firewall for private networks.

  2. Modify docker-compose.yml volumes:

    • C:/users/<username>/path-to-bitbucket/vcpa-web-api/scripts/initdb:/docker-entrypoint-initdb.d also change Docker setting

3. Make sure init.sh file format is in unix format.

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