Quickstart Guide

Get Parabricks up and running on a server and start using it in 10 minutes!

Step 1: Make sure installation requirements are met

The following are required to install Parabricks:

  • Access to the internet

  • nvidia-driver that supports cuda-9.0 or higher

  • nvidia-driver that supports cuda-10.0 or higher if you want to run deepvariant or cnnscorevariants

  • nvidia-docker or singularity version 2.6.1 or higher

  • Python 2.7 (Most Linux systems will already have this installed)

  • curl (Most Linux systems will already have this installed)

Step 2: Downloading Installation package

Contact info@parabricks.com to get an installation package for your GPU Server.

Step 3: Install Parabricks suite

Install the Parabricks package to your system:

# Step 1: Unzip the package.
$ tar -xzf parabricks.tar.gz
# Step 2: Run the installer
$ sudo ./parabricks/installer.py
# Step 3: verify your installation.
# This should display the parabricks version number:
$ pbrun version

After installation, pbrun is the executable that will start any tool in the Parabricks software suite. During installation you can choose to create a link at /usr/bin/pbrun to make it available for system wide access. Otherwise, you can access pbrun from your local installation directory (default: /opt/parabricks/pbrun).

Step 4: Example run

# Run the fq2bam tool, which aligns, co-ordinate sorts and marks duplicates
# in a pair-ended fastq file. Ref.fa is the bwa-indexed reference file
$ pbrun fq2bam --ref Ref.fa --in-fq sample_1.fq.gz sample_2.fq.gz --out-bam output.bam