Node Locked License, Debian Package Installation

Prerequisites

Installing Parabricks via the Debian/APT bare metal installer requires:

  • A working CUDA installation

  • Clara Parabricks Debian file (.deb). This file can be downloaded from the Clara Parabricks NGC registry

  • A license.bin generated from either the Nvidia Licensing Portal or for a Node Locked license

You can test whether you have CUDA installed by running the following:

nvidia-smi

If the command is not found, you do not receive a valid status message for your GPU or your CUDA version is older than:

  • CUDA 10.1 for non-Ampere GPUs

  • CUDA 11.0 for Ampere GPUs

then you will need to install CUDA. Instructions for doing so can be found at https://developer.nvidia.com/cuda-downloads. Once you have installed CUDA, you may proceed with the following steps.

To check if your system has Ampere GPUs, run the following:

nvidia-smi --query-gpu=name --format=csv,noheader

Any GPU labeled with the first letter A (e.g. 'Tesla A100', 'Tesla A40') is an Ampere GPU.

Software Installation

Install Anaconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x ./Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
## Add Conda path to your environment path
export PATH="<PATH-TO-CONDA>:$PATH"
## Restart your shell, or log out and back in
conda config --remove channels defaults

Create and activate a basic environment

## Create the conda environment and add the conda-forge repos
conda create -y --name parabricks -c conda-forge python=3.7 && \
conda activate parabricks && \
conda config --add channels bioconda

## Install dependencies into the new environment and then deactivate it.
conda install -y Cython matplotlib pysam wheel vcflib && \
conda deactivate

Create environments for extra tools

In order to use the optional extra tools (cnvkit, vcfqc, strelka & manta), the following Anaconda environments are required to be set up:

  • cnvkit (Optional):

conda create -y --name cnvkit_env -c conda-forge python=3.7 && \
conda activate cnvkit_env && \
conda config --add channels bioconda && \
conda install -y numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf networkx==2.5 pomegranate && \
conda deactivate
  • vcfqc (Optional):

conda create -y --name vcfqc -c conda-forge python=3.7 && \
conda activate vcfqc && \
pip install pandas==1.0.1 pysam==0.15.4 numpy==1.18.3 pytest jinja2 matplotlib seaborn upsetplot weasyprint bokeh selenium && \
conda deactivate
  • Manta & Strelka (Optional):

conda create -y --name manta_strelka -c conda-forge --no-default-packages python=2.7 && \
conda activate manta_strelka && \
conda deactivate

Installing the parabricks.deb package

# Install the software.
$ sudo apt install ./parabricks.deb

# Copy the license file.
$ sudo cp license.bin /usr/local/parabricks/

# Verify your installation.
# This should display the parabricks version number:
$ pbrun version

After installation the pbrun command will start any tool in the Parabricks software suite.

Note

If your machine has more GPUs than you have licenses, you will need to specify which, and how many, GPUs to use. For example, use the following flags to select only the first two GPUs:

CUDA_VISIBLE_DEVICES="0,1" pbrun [command and inputs]  --num-gpus 2