How to interactively access the data with BaseMount

Setting up your execution environment

We are setting up an Amazon instance located in the same region as the data for faster data transfer and lower latency.

• Launch an Amazon EC2 instance in the Frankfurt region (a.k.a. eu-central-1)

  • AMI: Ubuntu Server 16.04 LTS
  • Size depends on what you plan to do
    • RAM: 1.5GB or more for simple BaseMount access.

• Install BaseMount and samtools

 sudo bash -c "$(curl -L https://basemount.basespace.illumina.com/install)"

• Authenticate with BaseSpace to access the data remotely

 mkdir BaseSpace
 basemount --api-server=https://api.euc1.sh.basespace.illumina.com BaseSpace
 <Open the URL in the browser you usually use to log in to BaseSpace>
 
 # Check that you see the data
 ls "BaseSpace/Projects/Polaris 1 Diversity Cohort/AppResults/"

Accessing data via BaseMount

# HG01707 FASTQ files
ls -l "BaseSpace/Projects/Polaris 1 Diversity Cohort/Samples/HG01707/Files"

# HG01707 aligned data and variant calls
ls -l "BaseSpace/Projects/Polaris 1 Diversity Cohort/AppResults/HG01707/Files"

# Multi-sample VCF and metadata
ls -l "BaseSpace/Projects/Polaris 1 Diversity Cohort/AppResults/GVCF_Genotyper/Files"