This Version of Parabricks is no longer available: This documentation page is for reference only. Versions 3.8 and earlier have been deprecated. We encourage you to use the latest version, for which no license is required. If you need access to this version of Parabricks to continue an ongoing project, please contact the Parabricks team at parabricks-support@nvidia.com.
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.
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
# accept conda init and restart your shell
conda config --remove channels defaults
conda config --add channels bioconda
## Create the conda environment and add the conda-forge repos, install dependencies into the new environment and then deactivate it.
conda create -y --name parabricks -c conda-forge python=3.7 && \
conda activate parabricks && \
conda install -y -c conda-forge Cython matplotlib pysam wheel vcflib && \
conda deactivate
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 install -y -c conda-forge 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.
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