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 3: Configure your project information in the tracking database

3.2 Create the project in the tracking database

Previous3.1 List all projects in the tracking databaseNextStep 4: Upload sequencing data to your S3 bucket

Last updated 6 years ago

After login to the tracking database, users can add a new project into the database by using the below:

curl -sS -d project_name=${project_name} -d project_name_full=${project_name_full} -d project_desc=${projectdesc} -d project_center=${project_center} -d subproject_name=${subproject_name} "http://IP/v1/projects/add"

Create the project

POST http://IP/v1/projects/add

Request Body

Name
Type
Description

project_name

string

Abbreviations of the project name.

project_name_ful

string

Full project name.

projectdesc

string

Project description.

project_center

string

Where is the data generated / obtained from.

subproject_name

string

Subject project name.

IP

string

Public IP address.

{
    "status":"success",
    "project_id":"107"
}

The VCPA API will directly return a project ID (project_id) for this project.

command