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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  • Install AWS Command Line Interface
  • Set up the configuration file
  1. Step 1: Set up the Amazon Web Services (AWS) environment

1.4 Install AWS command line software for accessing S3 bucket via command line interface

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Last updated 6 years ago

Install AWS Command Line Interface

AWS command line interface (CLI) allow users to download or upload files to your S3 bucket in batch mode. Instructions on how to install the AWS CLI is shown below, note that this is different for different operating systems.

  • Linux–

  • Windows–

  • MacOS–

Users can verify if the AWS CLI has been installed properly by runningaws --version.

Set up the configuration file

After the software has been installed, users need to create the configuration file using the template below:

Type aws configure:

$ aws configureAWS Access Key ID: access_key_ID            ### input user's key ID here (the key generated in section 1.2) AWS Secret Access Key: secret_access_key    ### input user's access key (the key generated in section 1.2)Default region name: us-east-1              ### input the closet geographical location here

Users can verify the contents of the aws configure file by typing "aws configure list".

Adding the AWS CLI Executable to your Command Line Path
Adding the AWS CLI Executable to your Command Line Path
Adding the AWS CLI Executable to your Command Line Path