Install the Parabricks package to your system:
# Step 1: Unzip the package.
$ tar -xzf parabricks.tar.gz
# Step 2:
$ sudo ./parabricks/installer.py
# Step 3: verify your installation.
# This should display the parabricks version number:
$ pbrun version
After installation the pbrun executable 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).
If you have A100 GPUs, please make sure to pass –ampere to the step 2 above.
$ sudo ./parabricks/installer.py --ampere
If your machine has more GPUs than you have licenses, you need to specify how many GPUs to use and which GPUs to use. For example, use the following flags:
--gpu-devices 0,1 --num-gpus 2
Install the Parabricks package to your system:
# Step 1: Unzip the package.
$ tar -xzf parabricks.tar.gz
# Step 2 (Flexera License): Run the installer replacing [hostname] with the hostname of the license server.
$ sudo ./parabricks/installer.py --flexera-server [hostname]:7070
# Step 3: verify your installation.
# This should display the parabricks version number:
$ pbrun version
After installation the pbrun executable 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).
If you have A100 GPUs, please make sure to pass –ampere to the step 2 above.
$ sudo ./parabricks/installer.py --ampere
If your machine has more GPUs than you have pipelines licenses, you need to specify how many GPUs to use and which GPUs to use. For example, use the following flags:
--gpu-devices 0,1 --num-gpus 2
1. Log in to a machine with sudo access and singularity 3.0 or higher.
2. To download the software:
$ wget -O parabricks.tar.gz " < DOWNLOAD_LINK > "
3. Unzip the package
$ tar -xvzf parabricks.tar.gz
4. Do a local installation:$ mkdir localdir
$ sudo ./parabricks/installer.py --install-location localdir --container singularity
5. Everything will be installed in localdir/parabricks folder. Tar this folder.
$ cd localdir
$ tar -cvzf parabricks_install.tar.gz parabricks
6. and copy it to the node which will be used for testing and has singularity v3.x.
7. Untar the tar.gz file in some <INSTALL_DIR>$ cd <INSTALL_DIR>
$ tar -xvzf parabricks_install.tar.gz
Prerequisites
Installing Parabricks via the bare metal installer requires a working CUDA installation. You can test whether you have CUDA installed by running the following:
nvidia-smi
If the command is not found, or you do not receive a valid status message for your GPU or your CUDA version is older than the following:
CUDA 10.1 for non-Ampere GPUs CUDA 11.0 for Ampere GPUs (Not part of these instructions for now, ampere version will be available soon)
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 to the following steps.
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
## Restart your shell, or log out and back in
conda config --remove channels defaults
Create a basic environment and activate it
## Create the conda environment and add the conda-forge repos
conda create -y --name parabricks && \
conda activate parabricks && \
conda config --add channels conda-forge && \
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
(Optional) Create cnvkit_env
conda create -y --name cnvkit_env && \
conda activate cnvkit_env && \
conda config --add channels bioconda && \
conda config --add channels conda-forge && \
conda install -y numpy scipy pandas matplotlib reportlab biopython pyfaidx pysam pyvcf networkx==2.5 pomegranate && \
conda deactivate
(Optional) Create vcfqc
conda create -n vcfqc -y -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
Install the package using the command
sudo apt install <path to debian file>
Copy the license.bin
sudo cp pblicense.bin /usr/local/parabricks/
Update PATH
export PATH=/usr/local/parabricks${PATH:+:${PATH}}